diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html
index aeece214..151e0fb4 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.commands</a><span class="delimiter">/</span><span class="current">BlastN</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Blast</span><wbr></wbr><span><span>N</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">BlastN</a> : <a href="../-diamond-command-config/index.html">DiamondCommandConfig</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html">AdvancedGeneralOptionContainer</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-clustering-alignment-option-container/index.html">AdvancedClusteringAlignmentOptionContainer</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html">AdvancedQueryOptionContainer</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html">HiddenOptionContainer</a></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">interface </span><a href="index.html">BlastN</a> : <a href="../-diamond-command-config/index.html">DiamondCommandConfig</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html">AdvancedGeneralOptionContainer</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-clustering-alignment-option-container/index.html">AdvancedClusteringAlignmentOptionContainer</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html">AdvancedQueryOptionContainer</a>, <a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html">HiddenOptionContainer</a></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2783,7 +2783,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2798,7 +2798,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2828,7 +2828,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2873,7 +2873,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2918,7 +2918,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2993,7 +2993,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3008,7 +3008,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3038,7 +3038,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3068,7 +3068,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3083,7 +3083,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3113,7 +3113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3128,7 +3128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3143,7 +3143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3158,7 +3158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3173,7 +3173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3203,7 +3203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3218,7 +3218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3233,7 +3233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3248,7 +3248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3263,7 +3263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3278,7 +3278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3293,7 +3293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3308,7 +3308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3323,7 +3323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html
index 653bfa8c..9d59aa26 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2783,7 +2783,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2798,7 +2798,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2843,7 +2843,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3038,7 +3038,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3053,7 +3053,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3098,7 +3098,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3113,7 +3113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3128,7 +3128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3143,7 +3143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3158,7 +3158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3173,7 +3173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3188,7 +3188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3203,7 +3203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3233,7 +3233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3248,7 +3248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3278,7 +3278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3323,7 +3323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3338,7 +3338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3368,7 +3368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3383,7 +3383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3398,7 +3398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3503,7 +3503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3518,7 +3518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3533,7 +3533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3548,7 +3548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3563,7 +3563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3608,7 +3608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3623,7 +3623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3653,7 +3653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3683,7 +3683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3698,7 +3698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3728,7 +3728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3743,7 +3743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3758,7 +3758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3788,7 +3788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3803,7 +3803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3818,7 +3818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3833,7 +3833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3863,7 +3863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3953,7 +3953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3968,7 +3968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4013,7 +4013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4028,7 +4028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4043,7 +4043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4058,7 +4058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4073,7 +4073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4163,7 +4163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4178,7 +4178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4193,7 +4193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4208,7 +4208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4223,7 +4223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4238,7 +4238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4253,7 +4253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4268,7 +4268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4313,7 +4313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html
index a7728b76..f898ca51 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2783,7 +2783,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2798,7 +2798,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2843,7 +2843,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3038,7 +3038,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3053,7 +3053,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3098,7 +3098,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3113,7 +3113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3128,7 +3128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3143,7 +3143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3158,7 +3158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3173,7 +3173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3188,7 +3188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3203,7 +3203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3233,7 +3233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3248,7 +3248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3278,7 +3278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3323,7 +3323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3338,7 +3338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3368,7 +3368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3383,7 +3383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3398,7 +3398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3503,7 +3503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3518,7 +3518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3533,7 +3533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3548,7 +3548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3563,7 +3563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3608,7 +3608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3623,7 +3623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3653,7 +3653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3683,7 +3683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3698,7 +3698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3728,7 +3728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3743,7 +3743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3758,7 +3758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3788,7 +3788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3803,7 +3803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3818,7 +3818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3833,7 +3833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3863,7 +3863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3953,7 +3953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3968,7 +3968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4013,7 +4013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4028,7 +4028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4043,7 +4043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4058,7 +4058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4073,7 +4073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4163,7 +4163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4178,7 +4178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4193,7 +4193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4208,7 +4208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4223,7 +4223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4238,7 +4238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4253,7 +4253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4268,7 +4268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -4313,7 +4313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html
index 6ff8f528..d34beea3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2798,7 +2798,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster/index.html
index f3cf0a3e..9485c010 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-cluster/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2828,7 +2828,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2873,7 +2873,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2918,7 +2918,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2948,7 +2948,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2993,7 +2993,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3008,7 +3008,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3023,7 +3023,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3038,7 +3038,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3068,7 +3068,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html
index 4f084211..e2d58a02 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html
index f143589f..e73632bc 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2828,7 +2828,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2873,7 +2873,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2918,7 +2918,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2948,7 +2948,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2993,7 +2993,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3008,7 +3008,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3023,7 +3023,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3038,7 +3038,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3068,7 +3068,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html
index 96a2b778..3693a290 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html
index f50ae9c7..eccac684 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2783,7 +2783,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html
index 4df3c05f..234a71c2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2828,7 +2828,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2873,7 +2873,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2918,7 +2918,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2948,7 +2948,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2993,7 +2993,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3008,7 +3008,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3023,7 +3023,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3038,7 +3038,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3068,7 +3068,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html
index 71733fef..1b2bd793 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-index/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-index/index.html
index c3abf53a..ed391ed9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-index/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-make-index/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2798,7 +2798,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html
index a2c6a3ab..d08e6ce2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html
index 7b961231..9b0768e0 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html
index a75595c9..078a377a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2783,7 +2783,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2828,7 +2828,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2843,7 +2843,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2873,7 +2873,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2918,7 +2918,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2948,7 +2948,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2993,7 +2993,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3023,7 +3023,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html
index ec1cb8aa..2c0f8e83 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2558,7 +2558,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2768,7 +2768,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2783,7 +2783,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2813,7 +2813,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2828,7 +2828,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2843,7 +2843,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2858,7 +2858,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2873,7 +2873,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2888,7 +2888,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2903,7 +2903,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2918,7 +2918,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2933,7 +2933,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2948,7 +2948,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2963,7 +2963,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2978,7 +2978,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2993,7 +2993,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -3023,7 +3023,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-view/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-view/index.html
index 2b85b465..2056a419 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-view/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/-view/index.html
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2573,7 +2573,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2588,7 +2588,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2603,7 +2603,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2618,7 +2618,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2633,7 +2633,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2648,7 +2648,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2663,7 +2663,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2678,7 +2678,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2693,7 +2693,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2708,7 +2708,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2723,7 +2723,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2738,7 +2738,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2753,7 +2753,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2783,7 +2783,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/index.html
index b01a9e8a..90e99ab2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.commands/index.html
@@ -82,7 +82,7 @@ <h2 class="">Types</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="-blast-n/index.html">BlastN</a> : <a href="-diamond-command-config/index.html">DiamondCommandConfig</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html">AdvancedGeneralOptionContainer</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-clustering-alignment-option-container/index.html">AdvancedClusteringAlignmentOptionContainer</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html">AdvancedQueryOptionContainer</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html">HiddenOptionContainer</a></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../org.veupathdb.lib.cli.diamond/-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">interface </span><a href="-blast-n/index.html">BlastN</a> : <a href="-diamond-command-config/index.html">DiamondCommandConfig</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html">AdvancedGeneralOptionContainer</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-clustering-alignment-option-container/index.html">AdvancedClusteringAlignmentOptionContainer</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html">AdvancedQueryOptionContainer</a>, <a href="../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html">HiddenOptionContainer</a></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/-advanced-general-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/-advanced-general-option-container-impl.html
deleted file mode 100644
index 9732fe3a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/-advanced-general-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AdvancedGeneralOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/-advanced-general-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/AdvancedGeneralOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">AdvancedGeneralOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Advanced</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/file-buffer-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/file-buffer-size.html
deleted file mode 100644
index f3041aee..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/file-buffer-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>fileBufferSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/file-buffer-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/fileBufferSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">fileBufferSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>file</span><wbr></wbr><span>Buffer</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="file-buffer-size.html">fileBufferSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">File buffer size in bytes.</p><p class="paragraph">Flag = <code class="lang-kotlin">--file-buffer-size</code> Default = <code class="lang-kotlin">67108864</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/ignore-warnings.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/ignore-warnings.html
deleted file mode 100644
index 318aadb3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/ignore-warnings.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ignoreWarnings</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/ignore-warnings.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/ignoreWarnings/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">ignoreWarnings</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>ignore</span><wbr></wbr><span><span>Warnings</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ignore-warnings.html">ignoreWarnings</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Ignore warnings</p><p class="paragraph">Flag = <code class="lang-kotlin">--ignore-warnings</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/index.html
deleted file mode 100644
index 40bed3d9..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/index.html
+++ /dev/null
@@ -1,169 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AdvancedGeneralOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">AdvancedGeneralOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Advanced</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">AdvancedGeneralOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html">AdvancedGeneralOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="-1377007569%2FConstructors%2F769193423" anchor-label="AdvancedGeneralOptionContainerImpl" id="-1377007569%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-advanced-general-option-container-impl.html"><span>Advanced</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1377007569%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="739007672%2FProperties%2F769193423" anchor-label="fileBufferSize" id="739007672%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="file-buffer-size.html"><span>file</span><wbr></wbr><span>Buffer</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="739007672%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="file-buffer-size.html">fileBufferSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">File buffer size in bytes.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="188015852%2FProperties%2F769193423" anchor-label="ignoreWarnings" id="188015852%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ignore-warnings.html"><span>ignore</span><wbr></wbr><span><span>Warnings</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="188015852%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ignore-warnings.html">ignoreWarnings</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Ignore warnings</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1624113082%2FProperties%2F769193423" anchor-label="noParseSeqIDs" id="1624113082%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-parse-seq-i-ds.html"><span>no</span><wbr></wbr><span>Parse</span><wbr></wbr><span>Seq</span><wbr></wbr><span><span>IDs</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1624113082%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-parse-seq-i-ds.html">noParseSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Print raw seqids without parsing</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1410226785%2FProperties%2F769193423" anchor-label="noUnlink" id="1410226785%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-unlink.html"><span>no</span><wbr></wbr><span><span>Unlink</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1410226785%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-unlink.html">noUnlink</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not unlink temporary files.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-parse-seq-i-ds.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-parse-seq-i-ds.html
deleted file mode 100644
index 6a9cf12b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-parse-seq-i-ds.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noParseSeqIDs</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-parse-seq-i-ds.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/noParseSeqIDs/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noParseSeqIDs</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Parse</span><wbr></wbr><span>Seq</span><wbr></wbr><span><span>IDs</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-parse-seq-i-ds.html">noParseSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Print raw seqids without parsing</p><p class="paragraph">Flag = <code class="lang-kotlin">--no-parse-seqids</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-unlink.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-unlink.html
deleted file mode 100644
index dbfe5eb2..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-unlink.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noUnlink</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-unlink.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/noUnlink/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noUnlink</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span><span>Unlink</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-unlink.html">noUnlink</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Do not unlink temporary files.</p><p class="paragraph">Flag = <code class="lang-kotlin">--no-unlink</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/-advanced-query-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/-advanced-query-option-container-impl.html
deleted file mode 100644
index 4b13ebaf..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/-advanced-query-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AdvancedQueryOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/-advanced-query-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/AdvancedQueryOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">AdvancedQueryOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Advanced</span><wbr></wbr><span>Query</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/algo.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/algo.html
deleted file mode 100644
index 4e0a0253..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/algo.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>algo</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/algo.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/algo/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">algo</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>algo</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="algo.html">algo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Seed search algorithm (0=double-indexed/1=query-indexed/ctg=contiguous-seed)</p><p class="paragraph">TODO: enum this</p><p class="paragraph">Flag = <code class="lang-kotlin">--algo</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/align-long-reads.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/align-long-reads.html
deleted file mode 100644
index 698a83b5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/align-long-reads.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>alignLongReads</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/align-long-reads.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/alignLongReads/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">alignLongReads</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>align</span><wbr></wbr><span>Long</span><wbr></wbr><span><span>Reads</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="align-long-reads.html">alignLongReads</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Use chaining with extension.</p><p class="paragraph">Flag = <code class="lang-kotlin">--align-long-reads</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/band.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/band.html
deleted file mode 100644
index d65fa344..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/band.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>band</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/band.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/band/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">band</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>band</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="band.html">band</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Band for dynamic programming computation</p><p class="paragraph">Flag = <code class="lang-kotlin">--band</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/bootstrap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/bootstrap.html
deleted file mode 100644
index b8925404..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/bootstrap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>bootstrap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/bootstrap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/bootstrap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">bootstrap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>bootstrap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="bootstrap.html">bootstrap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--bootstrap</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-gap-scale.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-gap-scale.html
deleted file mode 100644
index cb394e49..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-gap-scale.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainPenGapScale</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-gap-scale.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/chainPenGapScale/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainPenGapScale</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chain</span><wbr></wbr><span>Pen</span><wbr></wbr><span>Gap</span><wbr></wbr><span><span>Scale</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chain-pen-gap-scale.html">chainPenGapScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Scaling factor for the chaining gap penalty.</p><p class="paragraph">Flag = <code class="lang-kotlin">--chain-pen-gap-scale</code> Default = <code class="lang-kotlin">0.8</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-skip-scale.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-skip-scale.html
deleted file mode 100644
index a51fcfae..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-skip-scale.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainPenSkipScale</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chain-pen-skip-scale.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/chainPenSkipScale/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainPenSkipScale</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chain</span><wbr></wbr><span>Pen</span><wbr></wbr><span>Skip</span><wbr></wbr><span><span>Scale</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chain-pen-skip-scale.html">chainPenSkipScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Scaling factor for the chaining skip penalty.</p><p class="paragraph">FLAG NAME TYPO EXISTS IN THE DIAMOND SOURCE CODE!</p><p class="paragraph">Flag = <code class="lang-kotlin">--chain-pen-skip-scalee</code> Default = <code class="lang-kotlin">0.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chaining-out.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chaining-out.html
deleted file mode 100644
index 1c4a3298..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chaining-out.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainingOut</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/chaining-out.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/chainingOut/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainingOut</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chaining</span><wbr></wbr><span><span>Out</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-out.html">chainingOut</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Use chaining without extension</p><p class="paragraph">Flag = <code class="lang-kotlin">--chaining-out</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/check-multi-target.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/check-multi-target.html
deleted file mode 100644
index fdeb964e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/check-multi-target.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>checkMultiTarget</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/check-multi-target.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/checkMultiTarget/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">checkMultiTarget</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>check</span><wbr></wbr><span>Multi</span><wbr></wbr><span><span>Target</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="check-multi-target.html">checkMultiTarget</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--check-multi-target</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/culling-overlap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/culling-overlap.html
deleted file mode 100644
index 3585303c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/culling-overlap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cullingOverlap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/culling-overlap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/cullingOverlap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cullingOverlap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>culling</span><wbr></wbr><span><span>Overlap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="culling-overlap.html">cullingOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum range overlap with higher scoring hit to delete a hit (default=50%)</p><p class="paragraph">Flag = <code class="lang-kotlin">--culling-overlap</code> Default = <code class="lang-kotlin">50.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/cut-bar.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/cut-bar.html
deleted file mode 100644
index f9f176f8..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/cut-bar.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cutBar</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/cut-bar.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/cutBar/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cutBar</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cut</span><wbr></wbr><span><span>Bar</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cut-bar.html">cutBar</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--cut-bar</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/extension.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/extension.html
deleted file mode 100644
index 578bdee5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/extension.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>extension</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/extension.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/extension/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">extension</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>extension</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="extension.html">extension</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-d-n-a-extension-algorithm/index.html">DNAExtensionAlgorithm</a></div><p class="paragraph">Extension algorithm (wfa, ksw=default)</p><p class="paragraph">Flag = <code class="lang-kotlin">--extension</code> Default = <code class="lang-kotlin">&quot;ksw&quot;</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map-query.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map-query.html
deleted file mode 100644
index baddc192..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map-query.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>familyMapQuery</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map-query.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/familyMapQuery/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">familyMapQuery</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>family</span><wbr></wbr><span>Map</span><wbr></wbr><span><span>Query</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-map-query.html">familyMapQuery</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">TODO: What is this? TODO: how is this used?</p><p class="paragraph">File = <code class="lang-kotlin">--family-map-query</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map.html
deleted file mode 100644
index 9301ec53..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>familyMap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/family-map.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/familyMap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">familyMap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>family</span><wbr></wbr><span><span>Map</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-map.html">familyMap</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">TODO: What is this, a file?</p><p class="paragraph">Flag = <code class="lang-kotlin">--family-map</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-masking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-masking.html
deleted file mode 100644
index 70543345..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-masking.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>freqMasking</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-masking.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/freqMasking/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">freqMasking</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>freq</span><wbr></wbr><span><span>Masking</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="freq-masking.html">freqMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Mask seeds based on frequency</p><p class="paragraph">Flag = <code class="lang-kotlin">--freq-masking</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-standard-deviation.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-standard-deviation.html
deleted file mode 100644
index e298ca7e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-standard-deviation.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>freqStandardDeviation</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/freq-standard-deviation.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/freqStandardDeviation/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">freqStandardDeviation</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>freq</span><wbr></wbr><span>Standard</span><wbr></wbr><span><span>Deviation</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="freq-standard-deviation.html">freqStandardDeviation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Number of standard deviations for ignoring frequent seeds.</p><p class="paragraph">Flag = <code class="lang-kotlin">--freq-sd</code> Default = <code class="lang-kotlin">0.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/gapped-filter-e-value.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/gapped-filter-e-value.html
deleted file mode 100644
index b28bb3cc..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/gapped-filter-e-value.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>gappedFilterEValue</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/gapped-filter-e-value.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/gappedFilterEValue/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">gappedFilterEValue</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>EValue</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-e-value.html">gappedFilterEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">E-value threshold for gapped filter (auto)</p><p class="paragraph">Flag = <code class="lang-kotlin">--gapped-filter-evalue</code> Default = <code class="lang-kotlin">-1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/heartbeat.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/heartbeat.html
deleted file mode 100644
index 1519d90b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/heartbeat.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>heartbeat</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/heartbeat.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/heartbeat/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">heartbeat</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>heartbeat</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="heartbeat.html">heartbeat</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--heartbeat</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/id2.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/id2.html
deleted file mode 100644
index 5e64113c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/id2.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>id2</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/id2.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/id2/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">id2</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>id2</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id2.html">id2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Minimum number of identities for stage 1 hit.</p><p class="paragraph">Flag = <code class="lang-kotlin">--id2</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/index.html
deleted file mode 100644
index 50fd5d46..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/index.html
+++ /dev/null
@@ -1,769 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AdvancedQueryOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">AdvancedQueryOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Advanced</span><wbr></wbr><span>Query</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">AdvancedQueryOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html">AdvancedQueryOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="161453679%2FConstructors%2F769193423" anchor-label="AdvancedQueryOptionContainerImpl" id="161453679%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-advanced-query-option-container-impl.html"><span>Advanced</span><wbr></wbr><span>Query</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="161453679%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="-640510718%2FProperties%2F769193423" anchor-label="algo" id="-640510718%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="algo.html"><span><span>algo</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-640510718%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="algo.html">algo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Seed search algorithm (0=double-indexed/1=query-indexed/ctg=contiguous-seed)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1835358841%2FProperties%2F769193423" anchor-label="alignLongReads" id="1835358841%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="align-long-reads.html"><span>align</span><wbr></wbr><span>Long</span><wbr></wbr><span><span>Reads</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1835358841%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="align-long-reads.html">alignLongReads</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use chaining with extension.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="654838624%2FProperties%2F769193423" anchor-label="band" id="654838624%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="band.html"><span><span>band</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="654838624%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="band.html">band</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Band for dynamic programming computation</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1239140393%2FProperties%2F769193423" anchor-label="bootstrap" id="-1239140393%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="bootstrap.html"><span><span>bootstrap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1239140393%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="bootstrap.html">bootstrap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="493811480%2FProperties%2F769193423" anchor-label="chainingOut" id="493811480%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chaining-out.html"><span>chaining</span><wbr></wbr><span><span>Out</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="493811480%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-out.html">chainingOut</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use chaining without extension</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1307051351%2FProperties%2F769193423" anchor-label="chainPenGapScale" id="-1307051351%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chain-pen-gap-scale.html"><span>chain</span><wbr></wbr><span>Pen</span><wbr></wbr><span>Gap</span><wbr></wbr><span><span>Scale</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1307051351%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chain-pen-gap-scale.html">chainPenGapScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Scaling factor for the chaining gap penalty.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1050107246%2FProperties%2F769193423" anchor-label="chainPenSkipScale" id="-1050107246%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chain-pen-skip-scale.html"><span>chain</span><wbr></wbr><span>Pen</span><wbr></wbr><span>Skip</span><wbr></wbr><span><span>Scale</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1050107246%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chain-pen-skip-scale.html">chainPenSkipScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Scaling factor for the chaining skip penalty.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1522140109%2FProperties%2F769193423" anchor-label="checkMultiTarget" id="-1522140109%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="check-multi-target.html"><span>check</span><wbr></wbr><span>Multi</span><wbr></wbr><span><span>Target</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1522140109%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="check-multi-target.html">checkMultiTarget</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1578612514%2FProperties%2F769193423" anchor-label="cullingOverlap" id="-1578612514%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="culling-overlap.html"><span>culling</span><wbr></wbr><span><span>Overlap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1578612514%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="culling-overlap.html">cullingOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum range overlap with higher scoring hit to delete a hit (default=50%)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1166908580%2FProperties%2F769193423" anchor-label="cutBar" id="1166908580%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cut-bar.html"><span>cut</span><wbr></wbr><span><span>Bar</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1166908580%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cut-bar.html">cutBar</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1004902618%2FProperties%2F769193423" anchor-label="extension" id="-1004902618%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="extension.html"><span><span>extension</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1004902618%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="extension.html">extension</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-d-n-a-extension-algorithm/index.html">DNAExtensionAlgorithm</a></div><div class="brief "><p class="paragraph">Extension algorithm (wfa, ksw=default)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-837379539%2FProperties%2F769193423" anchor-label="familyMap" id="-837379539%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="family-map.html"><span>family</span><wbr></wbr><span><span>Map</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-837379539%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-map.html">familyMap</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: What is this, a file?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-200239195%2FProperties%2F769193423" anchor-label="familyMapQuery" id="-200239195%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="family-map-query.html"><span>family</span><wbr></wbr><span>Map</span><wbr></wbr><span><span>Query</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-200239195%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-map-query.html">familyMapQuery</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: What is this? TODO: how is this used?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1594126745%2FProperties%2F769193423" anchor-label="freqMasking" id="-1594126745%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="freq-masking.html"><span>freq</span><wbr></wbr><span><span>Masking</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1594126745%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="freq-masking.html">freqMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Mask seeds based on frequency</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-99542695%2FProperties%2F769193423" anchor-label="freqStandardDeviation" id="-99542695%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="freq-standard-deviation.html"><span>freq</span><wbr></wbr><span>Standard</span><wbr></wbr><span><span>Deviation</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-99542695%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="freq-standard-deviation.html">freqStandardDeviation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Number of standard deviations for ignoring frequent seeds.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1146229208%2FProperties%2F769193423" anchor-label="gappedFilterEValue" id="1146229208%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="gapped-filter-e-value.html"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>EValue</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1146229208%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-e-value.html">gappedFilterEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">E-value threshold for gapped filter (auto)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2083065591%2FProperties%2F769193423" anchor-label="heartbeat" id="-2083065591%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="heartbeat.html"><span><span>heartbeat</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2083065591%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="heartbeat.html">heartbeat</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1328082450%2FProperties%2F769193423" anchor-label="id2" id="-1328082450%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="id2.html"><span><span>id2</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1328082450%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id2.html">id2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Minimum number of identities for stage 1 hit.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-760045268%2FProperties%2F769193423" anchor-label="linsearch" id="-760045268%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="linsearch.html"><span><span>linsearch</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-760045268%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="linsearch.html">linsearch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Only consider seed hits against longest target for identical seeds.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-206726111%2FProperties%2F769193423" anchor-label="linStage1" id="-206726111%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="lin-stage1.html"><span>lin</span><wbr></wbr><span><span>Stage1</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-206726111%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="lin-stage1.html">linStage1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Only consider seed hits against longest query for identical seeds.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1890033787%2FProperties%2F769193423" anchor-label="logEValueScale" id="1890033787%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="log-e-value-scale.html"><span>log</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Scale</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1890033787%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-e-value-scale.html">logEValueScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="159227876%2FProperties%2F769193423" anchor-label="minOrf" id="159227876%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="min-orf.html"><span>min</span><wbr></wbr><span><span>Orf</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="159227876%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-orf.html">minOrf</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Ignore translated sequences without an open reading frame of at least this length.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1426269186%2FProperties%2F769193423" anchor-label="mpInit" id="1426269186%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mp-init.html"><span>mp</span><wbr></wbr><span><span>Init</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1426269186%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-init.html">mpInit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Initialize multiprocessing run.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1858749331%2FProperties%2F769193423" anchor-label="mpQueryChunk" id="-1858749331%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mp-query-chunk.html"><span>mp</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Chunk</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1858749331%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-query-chunk.html">mpQueryChunk</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Process only a single query chunk as specified</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2047844%2FProperties%2F769193423" anchor-label="mpRecover" id="2047844%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mp-recover.html"><span>mp</span><wbr></wbr><span><span>Recover</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2047844%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-recover.html">mpRecover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Enable continuation of interrupted multiprocessing run.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="215577926%2FProperties%2F769193423" anchor-label="mpSelf" id="215577926%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mp-self.html"><span>mp</span><wbr></wbr><span><span>Self</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="215577926%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-self.html">mpSelf</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="703188217%2FProperties%2F769193423" anchor-label="multiprocessing" id="703188217%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="multiprocessing.html"><span><span>multiprocessing</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="703188217%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="multiprocessing.html">multiprocessing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">enable distributed-memory parallel processing</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="951968796%2FProperties%2F769193423" anchor-label="penalty" id="951968796%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="penalty.html"><span><span>penalty</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="951968796%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="penalty.html">penalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">BlastN mismatch penalty</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1261147409%2FProperties%2F769193423" anchor-label="queryOrSubjectCover" id="-1261147409%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="query-or-subject-cover.html"><span>query</span><wbr></wbr><span>Or</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>Cover</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1261147409%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-or-subject-cover.html">queryOrSubjectCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1261860503%2FProperties%2F769193423" anchor-label="queryParallelLimit" id="-1261860503%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="query-parallel-limit.html"><span>query</span><wbr></wbr><span>Parallel</span><wbr></wbr><span><span>Limit</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1261860503%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-parallel-limit.html">queryParallelLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1604630853%2FProperties%2F769193423" anchor-label="rangeCover" id="-1604630853%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="range-cover.html"><span>range</span><wbr></wbr><span><span>Cover</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1604630853%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="range-cover.html">rangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Percentage of query range to be covered for range culling (default=50%).</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1659915767%2FProperties%2F769193423" anchor-label="repetitionCutoff" id="1659915767%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="repetition-cutoff.html"><span>repetition</span><wbr></wbr><span><span>Cutoff</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1659915767%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="repetition-cutoff.html">repetitionCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Filter out top FLOAT fraction of repetitive minimizers.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-836386394%2FProperties%2F769193423" anchor-label="reward" id="-836386394%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="reward.html"><span><span>reward</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-836386394%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reward.html">reward</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">BlastN match reward</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-177757597%2FProperties%2F769193423" anchor-label="rocFile" id="-177757597%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="roc-file.html"><span>roc</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-177757597%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="roc-file.html">rocFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2145642279%2FProperties%2F769193423" anchor-label="samQueryLen" id="-2145642279%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="sam-query-len.html"><span>sam</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Len</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2145642279%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="sam-query-len.html">samQueryLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Add the query length to the SAM format (tag ZQ).</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-440104044%2FProperties%2F769193423" anchor-label="seedCut" id="-440104044%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="seed-cut.html"><span>seed</span><wbr></wbr><span><span>Cut</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-440104044%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seed-cut.html">seedCut</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Cutoff for seed complexity.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="973691128%2FProperties%2F769193423" anchor-label="shapeMask" id="973691128%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="shape-mask.html"><span>shape</span><wbr></wbr><span><span>Mask</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="973691128%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="shape-mask.html">shapeMask</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Seed shapes</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2045923174%2FProperties%2F769193423" anchor-label="stopMatchScore" id="2045923174%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="stop-match-score.html"><span>stop</span><wbr></wbr><span>Match</span><wbr></wbr><span><span>Score</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2045923174%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="stop-match-score.html">stopMatchScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Set the match score of stop codons against each other.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="606721125%2FProperties%2F769193423" anchor-label="targetIndexed" id="606721125%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="target-indexed.html"><span>target</span><wbr></wbr><span><span>Indexed</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="606721125%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-indexed.html">targetIndexed</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Enable target-indexed mode.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="914722388%2FProperties%2F769193423" anchor-label="taxonK" id="914722388%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="taxon-k.html"><span>taxon</span><wbr></wbr><span><span>K</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="914722388%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="taxon-k.html">taxonK</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Maximum number of targets to report per species.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-903930114%2FProperties%2F769193423" anchor-label="unalignedTargets" id="-903930114%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="unaligned-targets.html"><span>unaligned</span><wbr></wbr><span><span>Targets</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-903930114%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unaligned-targets.html">unalignedTargets</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: What is this?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1403895586%2FProperties%2F769193423" anchor-label="xDrop" id="-1403895586%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="x-drop.html"><span>x</span><wbr></wbr><span><span>Drop</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1403895586%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="x-drop.html">xDrop</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">xDrop for ungapped alignment.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2000927070%2FProperties%2F769193423" anchor-label="xmlBlOrdFormat" id="2000927070%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="xml-bl-ord-format.html"><span>xml</span><wbr></wbr><span>Bl</span><wbr></wbr><span>Ord</span><wbr></wbr><span><span>Format</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2000927070%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="xml-bl-ord-format.html">xmlBlOrdFormat</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use gnl|BL_ORD_ID| style format in XML output.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1381263332%2FProperties%2F769193423" anchor-label="zDrop" id="-1381263332%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="z-drop.html"><span>z</span><wbr></wbr><span><span>Drop</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1381263332%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="z-drop.html">zDrop</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">zDrop for gapped dna alignment</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/lin-stage1.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/lin-stage1.html
deleted file mode 100644
index 54397099..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/lin-stage1.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>linStage1</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/lin-stage1.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/linStage1/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">linStage1</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>lin</span><wbr></wbr><span><span>Stage1</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="lin-stage1.html">linStage1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Only consider seed hits against longest query for identical seeds.</p><p class="paragraph">Flag = <code class="lang-kotlin">--lin-stage1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/linsearch.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/linsearch.html
deleted file mode 100644
index 86b419f8..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/linsearch.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>linsearch</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/linsearch.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/linsearch/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">linsearch</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>linsearch</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="linsearch.html">linsearch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Only consider seed hits against longest target for identical seeds.</p><p class="paragraph">Flag = <code class="lang-kotlin">--linsearch</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/log-e-value-scale.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/log-e-value-scale.html
deleted file mode 100644
index 85f00f48..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/log-e-value-scale.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>logEValueScale</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/log-e-value-scale.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/logEValueScale/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">logEValueScale</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>log</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Scale</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-e-value-scale.html">logEValueScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--log-evalue-scale</code> Default = <code class="lang-kotlin">1.0 / std::log(2.0)</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/min-orf.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/min-orf.html
deleted file mode 100644
index 60401857..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/min-orf.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minOrf</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/min-orf.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/minOrf/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minOrf</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>min</span><wbr></wbr><span><span>Orf</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-orf.html">minOrf</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Ignore translated sequences without an open reading frame of at least this length.</p><p class="paragraph">Flag = <code class="lang-kotlin">--min-orf</code> | <code class="lang-kotlin">-l</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-init.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-init.html
deleted file mode 100644
index a79dcb51..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-init.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mpInit</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-init.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/mpInit/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mpInit</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mp</span><wbr></wbr><span><span>Init</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-init.html">mpInit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Initialize multiprocessing run.</p><p class="paragraph">Flag = <code class="lang-kotlin">--mp-init</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-query-chunk.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-query-chunk.html
deleted file mode 100644
index 264a91fd..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-query-chunk.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mpQueryChunk</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-query-chunk.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/mpQueryChunk/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mpQueryChunk</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mp</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Chunk</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-query-chunk.html">mpQueryChunk</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Process only a single query chunk as specified</p><p class="paragraph">Flag = <code class="lang-kotlin">--mp-query-chunk</code> Default = <code class="lang-kotlin">-1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-recover.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-recover.html
deleted file mode 100644
index bbcdd2e0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-recover.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mpRecover</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-recover.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/mpRecover/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mpRecover</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mp</span><wbr></wbr><span><span>Recover</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-recover.html">mpRecover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Enable continuation of interrupted multiprocessing run.</p><p class="paragraph">Flag = <code class="lang-kotlin">--mp-recover</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-self.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-self.html
deleted file mode 100644
index a6e2450f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-self.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mpSelf</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/mp-self.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/mpSelf/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mpSelf</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mp</span><wbr></wbr><span><span>Self</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mp-self.html">mpSelf</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--mp-self</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/multiprocessing.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/multiprocessing.html
deleted file mode 100644
index a6db3fc5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/multiprocessing.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>multiprocessing</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/multiprocessing.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/multiprocessing/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">multiprocessing</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>multiprocessing</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="multiprocessing.html">multiprocessing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">enable distributed-memory parallel processing</p><p class="paragraph">Flag = <code class="lang-kotlin">--multiprocessing</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/penalty.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/penalty.html
deleted file mode 100644
index 9b947653..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/penalty.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>penalty</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/penalty.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/penalty/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">penalty</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>penalty</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="penalty.html">penalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">BlastN mismatch penalty</p><p class="paragraph">Flag = <code class="lang-kotlin">--penalty</code> Default = <code class="lang-kotlin">-3</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-or-subject-cover.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-or-subject-cover.html
deleted file mode 100644
index d6c5aacd..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-or-subject-cover.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>queryOrSubjectCover</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-or-subject-cover.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/queryOrSubjectCover/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">queryOrSubjectCover</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>query</span><wbr></wbr><span>Or</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>Cover</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-or-subject-cover.html">queryOrSubjectCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--query-or-subject-cover</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-parallel-limit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-parallel-limit.html
deleted file mode 100644
index 79a5d7f3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-parallel-limit.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>queryParallelLimit</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/query-parallel-limit.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/queryParallelLimit/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">queryParallelLimit</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>query</span><wbr></wbr><span>Parallel</span><wbr></wbr><span><span>Limit</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-parallel-limit.html">queryParallelLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--query-parallel-limit</code> Default = <code class="lang-kotlin">3000000u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/range-cover.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/range-cover.html
deleted file mode 100644
index ef9b285f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/range-cover.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>rangeCover</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/range-cover.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/rangeCover/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">rangeCover</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>range</span><wbr></wbr><span><span>Cover</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="range-cover.html">rangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Percentage of query range to be covered for range culling (default=50%).</p><p class="paragraph">Flag = <code class="lang-kotlin">--range-cover</code> Default = <code class="lang-kotlin">50.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/repetition-cutoff.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/repetition-cutoff.html
deleted file mode 100644
index a3112a7f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/repetition-cutoff.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>repetitionCutoff</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/repetition-cutoff.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/repetitionCutoff/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">repetitionCutoff</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>repetition</span><wbr></wbr><span><span>Cutoff</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="repetition-cutoff.html">repetitionCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Filter out top FLOAT fraction of repetitive minimizers.</p><p class="paragraph">Flag = <code class="lang-kotlin">--repetition-cutoff</code> Default = <code class="lang-kotlin">0.0002</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/reward.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/reward.html
deleted file mode 100644
index 54c02d9b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/reward.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>reward</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/reward.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/reward/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">reward</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>reward</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reward.html">reward</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">BlastN match reward</p><p class="paragraph">Flag = <code class="lang-kotlin">--reward</code> Default = <code class="lang-kotlin">2</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/roc-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/roc-file.html
deleted file mode 100644
index e9c94326..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/roc-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>rocFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/roc-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/rocFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">rocFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>roc</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="roc-file.html">rocFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--roc-file</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/sam-query-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/sam-query-len.html
deleted file mode 100644
index 98cfaad7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/sam-query-len.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>samQueryLen</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/sam-query-len.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/samQueryLen/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">samQueryLen</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>sam</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Len</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="sam-query-len.html">samQueryLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Add the query length to the SAM format (tag ZQ).</p><p class="paragraph">Flag = <code class="lang-kotlin">--sam-query-len</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/seed-cut.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/seed-cut.html
deleted file mode 100644
index 22f5cd16..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/seed-cut.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>seedCut</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/seed-cut.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/seedCut/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">seedCut</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>seed</span><wbr></wbr><span><span>Cut</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seed-cut.html">seedCut</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Cutoff for seed complexity.</p><p class="paragraph">Flag = <code class="lang-kotlin">--seed-cut</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/shape-mask.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/shape-mask.html
deleted file mode 100644
index ad9b008d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/shape-mask.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>shapeMask</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/shape-mask.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/shapeMask/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">shapeMask</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>shape</span><wbr></wbr><span><span>Mask</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="shape-mask.html">shapeMask</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><p class="paragraph">Seed shapes</p><p class="paragraph">Flag = <code class="lang-kotlin">--shape-mask</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/stop-match-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/stop-match-score.html
deleted file mode 100644
index f870e227..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/stop-match-score.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>stopMatchScore</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/stop-match-score.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/stopMatchScore/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">stopMatchScore</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>stop</span><wbr></wbr><span>Match</span><wbr></wbr><span><span>Score</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="stop-match-score.html">stopMatchScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Set the match score of stop codons against each other.</p><p class="paragraph">Flag = <code class="lang-kotlin">--stop-match-score</code> Default = <code class="lang-kotlin">1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/target-indexed.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/target-indexed.html
deleted file mode 100644
index 8c8f6863..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/target-indexed.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>targetIndexed</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/target-indexed.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/targetIndexed/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">targetIndexed</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>target</span><wbr></wbr><span><span>Indexed</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-indexed.html">targetIndexed</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Enable target-indexed mode.</p><p class="paragraph">Flag = <code class="lang-kotlin">--target-indexed</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/taxon-k.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/taxon-k.html
deleted file mode 100644
index d5cef2cb..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/taxon-k.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>taxonK</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/taxon-k.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/taxonK/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">taxonK</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>taxon</span><wbr></wbr><span><span>K</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="taxon-k.html">taxonK</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Maximum number of targets to report per species.</p><p class="paragraph">Flag = <code class="lang-kotlin">--taxon-k</code> Default = <code class="lang-kotlin">0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/unaligned-targets.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/unaligned-targets.html
deleted file mode 100644
index 6f24db58..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/unaligned-targets.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>unalignedTargets</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/unaligned-targets.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/unalignedTargets/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">unalignedTargets</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>unaligned</span><wbr></wbr><span><span>Targets</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unaligned-targets.html">unalignedTargets</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">TODO: What is this?</p><p class="paragraph">Flag = <code class="lang-kotlin">--unaligned-targets</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/x-drop.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/x-drop.html
deleted file mode 100644
index 6bcaac76..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/x-drop.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>xDrop</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/x-drop.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/xDrop/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">xDrop</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>x</span><wbr></wbr><span><span>Drop</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="x-drop.html">xDrop</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">xDrop for ungapped alignment.</p><p class="paragraph">Flag = <code class="lang-kotlin">--xdrop</code> | <code class="lang-kotlin">-x</code> Default = <code class="lang-kotlin">12.3</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/xml-bl-ord-format.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/xml-bl-ord-format.html
deleted file mode 100644
index 122977b0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/xml-bl-ord-format.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>xmlBlOrdFormat</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/xml-bl-ord-format.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/xmlBlOrdFormat/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">xmlBlOrdFormat</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>xml</span><wbr></wbr><span>Bl</span><wbr></wbr><span>Ord</span><wbr></wbr><span><span>Format</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="xml-bl-ord-format.html">xmlBlOrdFormat</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Use gnl|BL_ORD_ID| style format in XML output.</p><p class="paragraph">Flag = <code class="lang-kotlin">--xml-blord-format</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
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-    </div>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/z-drop.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/z-drop.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>zDrop</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-    } else {
-        const savedDarkMode = JSON.parse(storage)
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
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-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
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-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/z-drop.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/zDrop/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AdvancedQueryOptionContainerImpl</a><span class="delimiter">/</span><span class="current">zDrop</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>z</span><wbr></wbr><span><span>Drop</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="z-drop.html">zDrop</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">zDrop for gapped dna alignment</p><p class="paragraph">Flag = <code class="lang-kotlin">--zdrop</code> | <code class="lang-kotlin">-z</code> Default = <code class="lang-kotlin">40</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
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-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/-aligner-clustering-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/-aligner-clustering-option-container-impl.html
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+++ /dev/null
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-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerClusteringOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
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-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
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-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/-aligner-clustering-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
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-    </div>
-    <div class="navigation-controls">
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-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringOptionContainerImpl/AlignerClusteringOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringOptionContainerImpl</a><span class="delimiter">/</span><span class="current">AlignerClusteringOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/approx-identity.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/approx-identity.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>approxIdentity</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/approx-identity.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
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-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringOptionContainerImpl/approxIdentity/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringOptionContainerImpl</a><span class="delimiter">/</span><span class="current">approxIdentity</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>approx</span><wbr></wbr><span><span>Identity</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="approx-identity.html">approxIdentity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum approximate identity % to report an alignment/to cluster sequences.</p><p class="paragraph">Flag = <code class="lang-kotlin">--approx-id</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/expect-value.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/expect-value.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>expectValue</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
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-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
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-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/expect-value.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-    <div class="navigation-controls">
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-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
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-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
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-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringOptionContainerImpl/expectValue/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringOptionContainerImpl</a><span class="delimiter">/</span><span class="current">expectValue</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>expect</span><wbr></wbr><span><span>Value</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="expect-value.html">expectValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Maximum e-value to report alignments.</p><p class="paragraph">Flag = <code class="lang-kotlin">--evalue</code> | <code class="lang-kotlin">-e</code> Default = <code class="lang-kotlin">0.001</code></p></div></div>
-</div>
-      <div class="footer">
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/extension-mode.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/extension-mode.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>extensionMode</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-    <div class="navigation--inner">
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-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/extension-mode.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
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-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringOptionContainerImpl/extensionMode/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringOptionContainerImpl</a><span class="delimiter">/</span><span class="current">extensionMode</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>extension</span><wbr></wbr><span><span>Mode</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="extension-mode.html">extensionMode</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-extension-mode/index.html">ExtensionMode</a></div><p class="paragraph">Extension mode.</p><p class="paragraph">Flag = <code class="lang-kotlin">--ext</code></p></div></div>
-</div>
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-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/index.html
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+++ /dev/null
@@ -1,169 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerClusteringOptionContainerImpl</title>
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-    <script>var pathToRoot = "../../../";</script>
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-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
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-</head>
-<body>
-    <div class="root">
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-    <div class="navigation--inner">
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-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
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-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
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-    <div class="navigation-controls">
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-    </div>
-</nav>
-        <div id="container">
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-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringOptionContainerImpl///PointingToDeclaration//769193423">
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-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">AlignerClusteringOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-option-container/index.html">AlignerClusteringOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="538172015%2FConstructors%2F769193423" anchor-label="AlignerClusteringOptionContainerImpl" id="538172015%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-clustering-option-container-impl.html"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="538172015%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="927706889%2FProperties%2F769193423" anchor-label="approxIdentity" id="927706889%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="approx-identity.html"><span>approx</span><wbr></wbr><span><span>Identity</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="927706889%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="approx-identity.html">approxIdentity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum approximate identity % to report an alignment/to cluster sequences.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1678672225%2FProperties%2F769193423" anchor-label="expectValue" id="1678672225%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="expect-value.html"><span>expect</span><wbr></wbr><span><span>Value</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1678672225%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="expect-value.html">expectValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum e-value to report alignments.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-116379721%2FProperties%2F769193423" anchor-label="extensionMode" id="-116379721%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="extension-mode.html"><span>extension</span><wbr></wbr><span><span>Mode</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-116379721%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="extension-mode.html">extensionMode</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-extension-mode/index.html">ExtensionMode</a></div><div class="brief "><p class="paragraph">Extension mode.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1193010406%2FProperties%2F769193423" anchor-label="motifMasking" id="-1193010406%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="motif-masking.html"><span>motif</span><wbr></wbr><span><span>Masking</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1193010406%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="motif-masking.html">motifMasking</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-motif-masking-algorithm/index.html">MotifMaskingAlgorithm</a></div><div class="brief "><p class="paragraph">Softmask abundant motifs (0/1)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
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-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
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-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/motif-masking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/motif-masking.html
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@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
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-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
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-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    <div class="navigation--inner">
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-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/motif-masking.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringOptionContainerImpl/motifMasking/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringOptionContainerImpl</a><span class="delimiter">/</span><span class="current">motifMasking</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>motif</span><wbr></wbr><span><span>Masking</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="motif-masking.html">motifMasking</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-motif-masking-algorithm/index.html">MotifMaskingAlgorithm</a></div><p class="paragraph">Softmask abundant motifs (0/1)</p><p class="paragraph">Flag = <code class="lang-kotlin">--motif-masking</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/-aligner-clustering-realign-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/-aligner-clustering-realign-option-container-impl.html
deleted file mode 100644
index d0f57602..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/-aligner-clustering-realign-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerClusteringRealignOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
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-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
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-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/-aligner-clustering-realign-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringRealignOptionContainerImpl/AlignerClusteringRealignOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringRealignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">AlignerClusteringRealignOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Realign</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/comp-based-stats.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/comp-based-stats.html
deleted file mode 100644
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/comp-based-stats.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>compBasedStats</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
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-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/comp-based-stats.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
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-    </div>
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-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringRealignOptionContainerImpl/compBasedStats/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringRealignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">compBasedStats</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>comp</span><wbr></wbr><span>Based</span><wbr></wbr><span><span>Stats</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="comp-based-stats.html">compBasedStats</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/index.html">CompositionBasedStats</a></div><p class="paragraph">Composition based statistics mode (0-4)</p><p class="paragraph">Flag = <code class="lang-kotlin">--comp-based-stats</code> Default = CompBasedStats.Hauser</p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/index.html
deleted file mode 100644
index 204b0ea0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/index.html
+++ /dev/null
@@ -1,184 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerClusteringRealignOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
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-        const savedDarkMode = JSON.parse(storage)
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringRealignOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">AlignerClusteringRealignOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Realign</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">AlignerClusteringRealignOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-realign-option-container/index.html">AlignerClusteringRealignOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="-1976783995%2FConstructors%2F769193423" anchor-label="AlignerClusteringRealignOptionContainerImpl" id="-1976783995%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-clustering-realign-option-container-impl.html"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Realign</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1976783995%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="1372479302%2FProperties%2F769193423" anchor-label="compBasedStats" id="1372479302%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="comp-based-stats.html"><span>comp</span><wbr></wbr><span>Based</span><wbr></wbr><span><span>Stats</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1372479302%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="comp-based-stats.html">compBasedStats</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/index.html">CompositionBasedStats</a></div><div class="brief "><p class="paragraph">Composition based statistics mode (0-4)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="227904323%2FProperties%2F769193423" anchor-label="masking" id="227904323%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="masking.html"><span><span>masking</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="227904323%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="masking.html">masking</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-masking-mode/index.html">MaskingMode</a></div><div class="brief "><p class="paragraph">Masking algorithm.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="252539787%2FProperties%2F769193423" anchor-label="mmseqsCompat" id="252539787%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mmseqs-compat.html"><span>mmseqs</span><wbr></wbr><span><span>Compat</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="252539787%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mmseqs-compat.html">mmseqsCompat</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">TODO: document this</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1516275597%2FProperties%2F769193423" anchor-label="noBlockSizeLimit" id="-1516275597%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-block-size-limit.html"><span>no</span><wbr></wbr><span>Block</span><wbr></wbr><span>Size</span><wbr></wbr><span><span>Limit</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1516275597%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-block-size-limit.html">noBlockSizeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">TODO: document this</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-849486451%2FProperties%2F769193423" anchor-label="softMasking" id="-849486451%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="soft-masking.html"><span>soft</span><wbr></wbr><span><span>Masking</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-849486451%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="soft-masking.html">softMasking</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-soft-masking-algorithm/index.html">SoftMaskingAlgorithm</a></div><div class="brief "><p class="paragraph">Soft masking.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/masking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/masking.html
deleted file mode 100644
index 4020708a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/masking.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>masking</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/masking.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringRealignOptionContainerImpl/masking/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringRealignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">masking</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>masking</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="masking.html">masking</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-masking-mode/index.html">MaskingMode</a></div><p class="paragraph">Masking algorithm.</p><p class="paragraph">Flag = <code class="lang-kotlin">--masking</code> Default = <a href="../../org.veupathdb.lib.cli.diamond.opts/-masking-mode/-tantan/index.html">MaskingMode.Tantan</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/mmseqs-compat.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/mmseqs-compat.html
deleted file mode 100644
index 6b1c9ad4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/mmseqs-compat.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mmseqsCompat</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/mmseqs-compat.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringRealignOptionContainerImpl/mmseqsCompat/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringRealignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mmseqsCompat</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mmseqs</span><wbr></wbr><span><span>Compat</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mmseqs-compat.html">mmseqsCompat</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">TODO: document this</p><p class="paragraph">Key = <code class="lang-kotlin">--mmseqs-compat</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/no-block-size-limit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/no-block-size-limit.html
deleted file mode 100644
index dcd7fe5b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/no-block-size-limit.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noBlockSizeLimit</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/no-block-size-limit.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringRealignOptionContainerImpl/noBlockSizeLimit/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringRealignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noBlockSizeLimit</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Block</span><wbr></wbr><span>Size</span><wbr></wbr><span><span>Limit</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-block-size-limit.html">noBlockSizeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">TODO: document this</p><p class="paragraph">Key = <code class="lang-kotlin">--no-block-size-limit</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/soft-masking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/soft-masking.html
deleted file mode 100644
index 09dc7d2e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/soft-masking.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>softMasking</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/soft-masking.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerClusteringRealignOptionContainerImpl/softMasking/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerClusteringRealignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">softMasking</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>soft</span><wbr></wbr><span><span>Masking</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="soft-masking.html">softMasking</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-soft-masking-algorithm/index.html">SoftMaskingAlgorithm</a></div><p class="paragraph">Soft masking.</p><p class="paragraph">Default value is subcommand dependent.</p><p class="paragraph">Flag = <code class="lang-kotlin">--soft-masking</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/-aligner-general-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/-aligner-general-option-container-impl.html
deleted file mode 100644
index 2738c4f1..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/-aligner-general-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerGeneralOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/-aligner-general-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/AlignerGeneralOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">AlignerGeneralOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file-format.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file-format.html
deleted file mode 100644
index eddd27df..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file-format.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>alignedFileFormat</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file-format.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/alignedFileFormat/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">alignedFileFormat</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>aligned</span><wbr></wbr><span>File</span><wbr></wbr><span><span>Format</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="aligned-file-format.html">alignedFileFormat</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-query-file-format/index.html">QueryFileFormat</a></div><p class="paragraph">Format of aligned query file.</p><p class="paragraph">Flag = <code class="lang-kotlin">--alfmt</code> Default = <a href="../../org.veupathdb.lib.cli.diamond.opts/-query-file-format/-f-a-s-t-a/index.html">QueryFileFormat.FASTA</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file.html
deleted file mode 100644
index b76b931e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>alignedFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/aligned-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/alignedFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">alignedFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>aligned</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="aligned-file.html">alignedFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">File or aligned queries</p><p class="paragraph">Flag = <code class="lang-kotlin">--al</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/block-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/block-size.html
deleted file mode 100644
index bfb08422..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/block-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>blockSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/block-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/blockSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">blockSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>block</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="block-size.html">blockSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Sequence block size in billions of letters.</p><p class="paragraph">Flag = <code class="lang-kotlin">--block-size</code> | <code class="lang-kotlin">-b</code> Default = <code class="lang-kotlin">2.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/compress.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/compress.html
deleted file mode 100644
index e62529b0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/compress.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>compress</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/compress.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/compress/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">compress</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>compress</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="compress.html">compress</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-compression/index.html">Compression</a></div><p class="paragraph">Compression for output files.</p><p class="paragraph">Flag = <code class="lang-kotlin">--compress</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/custom-matrix.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/custom-matrix.html
deleted file mode 100644
index 4c9870f0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/custom-matrix.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>customMatrix</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/custom-matrix.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/customMatrix/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">customMatrix</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>custom</span><wbr></wbr><span><span>Matrix</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="custom-matrix.html">customMatrix</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">File containing custom scoring matrix.</p><p class="paragraph">Flag = <code class="lang-kotlin">--custom-matrix</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/frame-shift-penalty.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/frame-shift-penalty.html
deleted file mode 100644
index 5c10ce64..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/frame-shift-penalty.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>frameShiftPenalty</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/frame-shift-penalty.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/frameShiftPenalty/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">frameShiftPenalty</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>frame</span><wbr></wbr><span>Shift</span><wbr></wbr><span><span>Penalty</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="frame-shift-penalty.html">frameShiftPenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Frame shift penalty (default=disabled)</p><p class="paragraph">Flag = <code class="lang-kotlin">--frameshift</code> | <code class="lang-kotlin">-F</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-extend-penalty.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-extend-penalty.html
deleted file mode 100644
index 0a4a54b2..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-extend-penalty.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>gapExtendPenalty</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-extend-penalty.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/gapExtendPenalty/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">gapExtendPenalty</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>gap</span><wbr></wbr><span>Extend</span><wbr></wbr><span><span>Penalty</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gap-extend-penalty.html">gapExtendPenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Gap extension penalty.</p><p class="paragraph">Flag = <code class="lang-kotlin">--gapextend</code> Default = <code class="lang-kotlin">-1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-open-penalty.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-open-penalty.html
deleted file mode 100644
index 7910853b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-open-penalty.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>gapOpenPenalty</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/gap-open-penalty.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/gapOpenPenalty/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">gapOpenPenalty</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>gap</span><wbr></wbr><span>Open</span><wbr></wbr><span><span>Penalty</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gap-open-penalty.html">gapOpenPenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Gap open penalty.</p><p class="paragraph">Flag = <code class="lang-kotlin">--gapopen</code> Default = <code class="lang-kotlin">-1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/global-ranking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/global-ranking.html
deleted file mode 100644
index b1ef39aa..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/global-ranking.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>globalRanking</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/global-ranking.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/globalRanking/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">globalRanking</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>global</span><wbr></wbr><span><span>Ranking</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="global-ranking.html">globalRanking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Number of targets for global ranking.</p><p class="paragraph">Type = <code class="lang-kotlin">--global-ranking</code> | <code class="lang-kotlin">-g</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-all-subject-i-ds.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-all-subject-i-ds.html
deleted file mode 100644
index 0db8e71e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-all-subject-i-ds.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>includeAllSubjectIDs</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-all-subject-i-ds.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/includeAllSubjectIDs/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">includeAllSubjectIDs</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>include</span><wbr></wbr><span>All</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>IDs</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="include-all-subject-i-ds.html">includeAllSubjectIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Include all subject ids in DAA file</p><p class="paragraph">Flag = <code class="lang-kotlin">--sallseqid</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-full-subject-titles.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-full-subject-titles.html
deleted file mode 100644
index 825e2c9a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-full-subject-titles.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>includeFullSubjectTitles</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/include-full-subject-titles.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/includeFullSubjectTitles/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">includeFullSubjectTitles</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>include</span><wbr></wbr><span>Full</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>Titles</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="include-full-subject-titles.html">includeFullSubjectTitles</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Include full subject titles in DAA file.</p><p class="paragraph">Flag = <code class="lang-kotlin">--salltitles</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index-chunks.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index-chunks.html
deleted file mode 100644
index 3a131d6d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index-chunks.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>indexChunks</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index-chunks.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/indexChunks/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">indexChunks</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>index</span><wbr></wbr><span><span>Chunks</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="index-chunks.html">indexChunks</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Number of chunks for index processing.</p><p class="paragraph">Flag = <code class="lang-kotlin">--index-chunks</code> | <code class="lang-kotlin">-c</code> Default = <code class="lang-kotlin">4</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index.html
deleted file mode 100644
index fd471b2c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index.html
+++ /dev/null
@@ -1,619 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerGeneralOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">AlignerGeneralOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">AlignerGeneralOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-aligner-general-option-container/index.html">AlignerGeneralOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="14159681%2FConstructors%2F769193423" anchor-label="AlignerGeneralOptionContainerImpl" id="14159681%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-general-option-container-impl.html"><span>Aligner</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="14159681%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="880932279%2FProperties%2F769193423" anchor-label="alignedFile" id="880932279%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="aligned-file.html"><span>aligned</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="880932279%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="aligned-file.html">alignedFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">File or aligned queries</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="232859136%2FProperties%2F769193423" anchor-label="alignedFileFormat" id="232859136%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="aligned-file-format.html"><span>aligned</span><wbr></wbr><span>File</span><wbr></wbr><span><span>Format</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="232859136%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="aligned-file-format.html">alignedFileFormat</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-query-file-format/index.html">QueryFileFormat</a></div><div class="brief "><p class="paragraph">Format of aligned query file.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1507483703%2FProperties%2F769193423" anchor-label="blockSize" id="-1507483703%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="block-size.html"><span>block</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1507483703%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="block-size.html">blockSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Sequence block size in billions of letters.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1820566303%2FProperties%2F769193423" anchor-label="compress" id="-1820566303%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="compress.html"><span><span>compress</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1820566303%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="compress.html">compress</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-compression/index.html">Compression</a></div><div class="brief "><p class="paragraph">Compression for output files.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1613935793%2FProperties%2F769193423" anchor-label="customMatrix" id="1613935793%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="custom-matrix.html"><span>custom</span><wbr></wbr><span><span>Matrix</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1613935793%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="custom-matrix.html">customMatrix</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">File containing custom scoring matrix.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1129463037%2FProperties%2F769193423" anchor-label="frameShiftPenalty" id="-1129463037%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="frame-shift-penalty.html"><span>frame</span><wbr></wbr><span>Shift</span><wbr></wbr><span><span>Penalty</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1129463037%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="frame-shift-penalty.html">frameShiftPenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Frame shift penalty (default=disabled)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1002944842%2FProperties%2F769193423" anchor-label="gapExtendPenalty" id="1002944842%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="gap-extend-penalty.html"><span>gap</span><wbr></wbr><span>Extend</span><wbr></wbr><span><span>Penalty</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1002944842%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gap-extend-penalty.html">gapExtendPenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Gap extension penalty.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1785651066%2FProperties%2F769193423" anchor-label="gapOpenPenalty" id="1785651066%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="gap-open-penalty.html"><span>gap</span><wbr></wbr><span>Open</span><wbr></wbr><span><span>Penalty</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1785651066%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gap-open-penalty.html">gapOpenPenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Gap open penalty.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="644851076%2FProperties%2F769193423" anchor-label="globalRanking" id="644851076%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="global-ranking.html"><span>global</span><wbr></wbr><span><span>Ranking</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="644851076%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="global-ranking.html">globalRanking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Number of targets for global ranking.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1286848034%2FProperties%2F769193423" anchor-label="includeAllSubjectIDs" id="-1286848034%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="include-all-subject-i-ds.html"><span>include</span><wbr></wbr><span>All</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>IDs</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1286848034%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="include-all-subject-i-ds.html">includeAllSubjectIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Include all subject ids in DAA file</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="920849587%2FProperties%2F769193423" anchor-label="includeFullSubjectTitles" id="920849587%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="include-full-subject-titles.html"><span>include</span><wbr></wbr><span>Full</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>Titles</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="920849587%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="include-full-subject-titles.html">includeFullSubjectTitles</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Include full subject titles in DAA file.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="786109343%2FProperties%2F769193423" anchor-label="indexChunks" id="786109343%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="index-chunks.html"><span>index</span><wbr></wbr><span><span>Chunks</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="786109343%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="index-chunks.html">indexChunks</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of chunks for index processing.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-82418307%2FProperties%2F769193423" anchor-label="iterate" id="-82418307%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="iterate.html"><span><span>iterate</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-82418307%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="iterate.html">iterate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sensitivity/index.html">Sensitivity</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Iterated search with increasing sensitivity.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-880702250%2FProperties%2F769193423" anchor-label="longReads" id="-880702250%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="long-reads.html"><span>long</span><wbr></wbr><span><span>Reads</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-880702250%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="long-reads.html">longReads</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Short for <code class="lang-kotlin">--range-culling --top 10 -F 15</code>.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="104456930%2FProperties%2F769193423" anchor-label="matrix" id="104456930%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="matrix.html"><span><span>matrix</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="104456930%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="matrix.html">matrix</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-score-matrix/index.html">ScoreMatrix</a></div><div class="brief "><p class="paragraph">Score matrix for protein alignment.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1286368987%2FProperties%2F769193423" anchor-label="maxHSPs" id="-1286368987%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="max-h-s-ps.html"><span>max</span><wbr></wbr><span><span>HSPs</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1286368987%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-h-s-ps.html">maxHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Maximum number of HSPs per target sequence to report for each query.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2039176785%2FProperties%2F769193423" anchor-label="minimumIdentityPercentage" id="2039176785%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="minimum-identity-percentage.html"><span>minimum</span><wbr></wbr><span>Identity</span><wbr></wbr><span><span>Percentage</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2039176785%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimum-identity-percentage.html">minimumIdentityPercentage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum identity percentage to report an alignment.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-836734304%2FProperties%2F769193423" anchor-label="minimumQueryCoverPercentage" id="-836734304%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="minimum-query-cover-percentage.html"><span>minimum</span><wbr></wbr><span>Query</span><wbr></wbr><span>Cover</span><wbr></wbr><span><span>Percentage</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-836734304%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimum-query-cover-percentage.html">minimumQueryCoverPercentage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum query cover percentage to report an alignment.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2021132292%2FProperties%2F769193423" anchor-label="minimumSubjectCoverPercentage" id="2021132292%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="minimum-subject-cover-percentage.html"><span>minimum</span><wbr></wbr><span>Subject</span><wbr></wbr><span>Cover</span><wbr></wbr><span><span>Percentage</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2021132292%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimum-subject-cover-percentage.html">minimumSubjectCoverPercentage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum subject cover percentage to report an alignment.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-144058717%2FProperties%2F769193423" anchor-label="minScore" id="-144058717%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="min-score.html"><span>min</span><wbr></wbr><span><span>Score</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-144058717%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-score.html">minScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum bit score to report alignments (overrides e-value setting).</p></div></div></div>
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-<a data-name="2122663830%2FProperties%2F769193423" anchor-label="noSelfHits" id="2122663830%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-self-hits.html"><span>no</span><wbr></wbr><span>Self</span><wbr></wbr><span><span>Hits</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2122663830%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-self-hits.html">noSelfHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Suppress reporting of identical self hits.</p></div></div></div>
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-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="parallel-tmp-dir.html"><span>parallel</span><wbr></wbr><span>Tmp</span><wbr></wbr><span><span>Dir</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1004286790%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="parallel-tmp-dir.html">parallelTmpDir</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Directory for temporary files used by multiprocessing.</p></div></div></div>
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-<a data-name="1408278383%2FProperties%2F769193423" anchor-label="query" id="1408278383%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="query.html"><span><span>query</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1408278383%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query.html">query</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Input query file.</p></div></div></div>
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-<a data-name="246237486%2FProperties%2F769193423" anchor-label="queryGenCode" id="246237486%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="query-gen-code.html"><span>query</span><wbr></wbr><span>Gen</span><wbr></wbr><span><span>Code</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="246237486%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-gen-code.html">queryGenCode</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-translator-gen-code/index.html">TranslatorGenCode</a></div><div class="brief "><p class="paragraph">Genetic code to use to translate query.</p></div></div></div>
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-              </div>
-            </div>
-          </div>
-<a data-name="-1677705936%2FProperties%2F769193423" anchor-label="rangeCulling" id="-1677705936%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="range-culling.html"><span>range</span><wbr></wbr><span><span>Culling</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1677705936%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="range-culling.html">rangeCulling</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restrict hit culling to overlapping query ranges.</p></div></div></div>
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-<a data-name="-1716247649%2FProperties%2F769193423" anchor-label="seqIdList" id="-1716247649%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="seq-id-list.html"><span>seq</span><wbr></wbr><span>Id</span><wbr></wbr><span><span>List</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1716247649%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seq-id-list.html">seqIdList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filter the database by list of accessions.</p></div></div></div>
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-<a data-name="1284821111%2FProperties%2F769193423" anchor-label="skipMissingSeqIDs" id="1284821111%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="skip-missing-seq-i-ds.html"><span>skip</span><wbr></wbr><span>Missing</span><wbr></wbr><span>Seq</span><wbr></wbr><span><span>IDs</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1284821111%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="skip-missing-seq-i-ds.html">skipMissingSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Ignore accessions missing in the database.</p></div></div></div>
-                </div>
-              </div>
-            </div>
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-<a data-name="966320189%2FProperties%2F769193423" anchor-label="strand" id="966320189%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="strand.html"><span><span>strand</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="966320189%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="strand.html">strand</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-query-strand/index.html">QueryStrand</a></div><div class="brief "><p class="paragraph">Query strands to search.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-745456323%2FProperties%2F769193423" anchor-label="swipe" id="-745456323%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="swipe.html"><span><span>swipe</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-745456323%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="swipe.html">swipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Exhaustive alignment against all database sequences.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1867708755%2FProperties%2F769193423" anchor-label="taxonExclude" id="1867708755%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="taxon-exclude.html"><span>taxon</span><wbr></wbr><span><span>Exclude</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1867708755%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="taxon-exclude.html">taxonExclude</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Exclude list of taxon ids.</p></div></div></div>
-                </div>
-              </div>
-            </div>
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-<a data-name="-1173150545%2FProperties%2F769193423" anchor-label="taxonList" id="-1173150545%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="taxon-list.html"><span>taxon</span><wbr></wbr><span><span>List</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1173150545%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="taxon-list.html">taxonList</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Restrict search to list of taxon ids.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1343171839%2FProperties%2F769193423" anchor-label="unal" id="1343171839%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="unal.html"><span><span>unal</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1343171839%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unal.html">unal</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Report unaligned queries.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2141694640%2FProperties%2F769193423" anchor-label="unalignedFile" id="-2141694640%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="unaligned-file.html"><span>unaligned</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2141694640%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unaligned-file.html">unalignedFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">File for unaligned queries.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1362252071%2FProperties%2F769193423" anchor-label="unalignedFileFormat" id="-1362252071%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="unaligned-file-format.html"><span>unaligned</span><wbr></wbr><span>File</span><wbr></wbr><span><span>Format</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1362252071%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unaligned-file-format.html">unalignedFileFormat</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-query-file-format/index.html">QueryFileFormat</a></div><div class="brief "><p class="paragraph">Format of unaligned query file.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/iterate.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/iterate.html
deleted file mode 100644
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/iterate.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>iterate</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/iterate.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/iterate/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">iterate</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>iterate</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="iterate.html">iterate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sensitivity/index.html">Sensitivity</a><span class="token operator">&gt;</span></div><p class="paragraph">Iterated search with increasing sensitivity.</p><p class="paragraph">Flag = <code class="lang-kotlin">--iterate</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/long-reads.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/long-reads.html
deleted file mode 100644
index 3685e90c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/long-reads.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>longReads</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/long-reads.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/longReads/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">longReads</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>long</span><wbr></wbr><span><span>Reads</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="long-reads.html">longReads</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Short for <code class="lang-kotlin">--range-culling --top 10 -F 15</code>.</p><p class="paragraph">TODO: conflict detection!</p><p class="paragraph">Flag = <code class="lang-kotlin">--long-reads</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/matrix.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/matrix.html
deleted file mode 100644
index 0dc85b21..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/matrix.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>matrix</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/matrix.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/matrix/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">matrix</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>matrix</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="matrix.html">matrix</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-score-matrix/index.html">ScoreMatrix</a></div><p class="paragraph">Score matrix for protein alignment.</p><p class="paragraph">Flag = <code class="lang-kotlin">--matrix</code> Default = <a href="../../org.veupathdb.lib.cli.diamond.opts/-score-matrix/-b-l-o-s-u-m62/index.html">ScoreMatrix.BLOSUM62</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/max-h-s-ps.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/max-h-s-ps.html
deleted file mode 100644
index c0421bf5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/max-h-s-ps.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>maxHSPs</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/max-h-s-ps.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/maxHSPs/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">maxHSPs</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>max</span><wbr></wbr><span><span>HSPs</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-h-s-ps.html">maxHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Maximum number of HSPs per target sequence to report for each query.</p><p class="paragraph">Flag = <code class="lang-kotlin">--max-hsps</code> Default = <code class="lang-kotlin">1u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/min-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/min-score.html
deleted file mode 100644
index 9c6fe85f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/min-score.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minScore</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/min-score.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/minScore/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minScore</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>min</span><wbr></wbr><span><span>Score</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-score.html">minScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum bit score to report alignments (overrides e-value setting).</p><p class="paragraph">Flag = <code class="lang-kotlin">--min-score</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-identity-percentage.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-identity-percentage.html
deleted file mode 100644
index a4c4676e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-identity-percentage.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minimumIdentityPercentage</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-identity-percentage.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/minimumIdentityPercentage/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minimumIdentityPercentage</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>minimum</span><wbr></wbr><span>Identity</span><wbr></wbr><span><span>Percentage</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimum-identity-percentage.html">minimumIdentityPercentage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum identity percentage to report an alignment.</p><p class="paragraph">Flag = <code class="lang-kotlin">--id</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-query-cover-percentage.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-query-cover-percentage.html
deleted file mode 100644
index c1f8efe5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-query-cover-percentage.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minimumQueryCoverPercentage</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-query-cover-percentage.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/minimumQueryCoverPercentage/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minimumQueryCoverPercentage</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>minimum</span><wbr></wbr><span>Query</span><wbr></wbr><span>Cover</span><wbr></wbr><span><span>Percentage</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimum-query-cover-percentage.html">minimumQueryCoverPercentage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum query cover percentage to report an alignment.</p><p class="paragraph">Flag = <code class="lang-kotlin">--query-cover</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-subject-cover-percentage.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-subject-cover-percentage.html
deleted file mode 100644
index a545889e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-subject-cover-percentage.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minimumSubjectCoverPercentage</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/minimum-subject-cover-percentage.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/minimumSubjectCoverPercentage/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minimumSubjectCoverPercentage</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>minimum</span><wbr></wbr><span>Subject</span><wbr></wbr><span>Cover</span><wbr></wbr><span><span>Percentage</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimum-subject-cover-percentage.html">minimumSubjectCoverPercentage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum subject cover percentage to report an alignment.</p><p class="paragraph">Flag = <code class="lang-kotlin">--subject-cover</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/no-self-hits.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/no-self-hits.html
deleted file mode 100644
index 3fd8c4d4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/no-self-hits.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noSelfHits</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/no-self-hits.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/noSelfHits/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noSelfHits</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Self</span><wbr></wbr><span><span>Hits</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-self-hits.html">noSelfHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Suppress reporting of identical self hits.</p><p class="paragraph">Flag = <code class="lang-kotlin">--no-self-hits</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/parallel-tmp-dir.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/parallel-tmp-dir.html
deleted file mode 100644
index 2b9779ca..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/parallel-tmp-dir.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>parallelTmpDir</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/parallel-tmp-dir.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/parallelTmpDir/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">parallelTmpDir</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>parallel</span><wbr></wbr><span>Tmp</span><wbr></wbr><span><span>Dir</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="parallel-tmp-dir.html">parallelTmpDir</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Directory for temporary files used by multiprocessing.</p><p class="paragraph">Flag = <code class="lang-kotlin">--parallel-tmpdir</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query-gen-code.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query-gen-code.html
deleted file mode 100644
index 5468a985..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query-gen-code.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>queryGenCode</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query-gen-code.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/queryGenCode/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">queryGenCode</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>query</span><wbr></wbr><span>Gen</span><wbr></wbr><span><span>Code</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-gen-code.html">queryGenCode</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-translator-gen-code/index.html">TranslatorGenCode</a></div><p class="paragraph">Genetic code to use to translate query.</p><p class="paragraph">Flag = <code class="lang-kotlin">--query-gencode</code> Default = <a href="../../org.veupathdb.lib.cli.diamond.opts/-translator-gen-code/-standard/index.html">TranslatorGenCode.Standard</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query.html
deleted file mode 100644
index 0650d498..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>query</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/query.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/query/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">query</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>query</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query.html">query</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a><span class="token operator">&gt;</span></div><p class="paragraph">Input query file.</p><p class="paragraph">Flag = <code class="lang-kotlin">--query</code> | <code class="lang-kotlin">-q</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/range-culling.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/range-culling.html
deleted file mode 100644
index 28eebf50..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/range-culling.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>rangeCulling</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/range-culling.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/rangeCulling/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">rangeCulling</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>range</span><wbr></wbr><span><span>Culling</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="range-culling.html">rangeCulling</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Restrict hit culling to overlapping query ranges.</p><p class="paragraph">Flag = <code class="lang-kotlin">--range-culling</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/seq-id-list.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/seq-id-list.html
deleted file mode 100644
index 039c2ae3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/seq-id-list.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>seqIdList</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/seq-id-list.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/seqIdList/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">seqIdList</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>seq</span><wbr></wbr><span>Id</span><wbr></wbr><span><span>List</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seq-id-list.html">seqIdList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Filter the database by list of accessions.</p><p class="paragraph">Flag = <code class="lang-kotlin">--seqidlist</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/skip-missing-seq-i-ds.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/skip-missing-seq-i-ds.html
deleted file mode 100644
index b0f4771f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/skip-missing-seq-i-ds.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>skipMissingSeqIDs</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/skip-missing-seq-i-ds.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/skipMissingSeqIDs/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">skipMissingSeqIDs</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>skip</span><wbr></wbr><span>Missing</span><wbr></wbr><span>Seq</span><wbr></wbr><span><span>IDs</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="skip-missing-seq-i-ds.html">skipMissingSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Ignore accessions missing in the database.</p><p class="paragraph">Flag = <code class="lang-kotlin">--skip-missing-seqids</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/strand.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/strand.html
deleted file mode 100644
index c9178a1b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/strand.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>strand</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/strand.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/strand/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">strand</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>strand</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="strand.html">strand</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-query-strand/index.html">QueryStrand</a></div><p class="paragraph">Query strands to search.</p><p class="paragraph">Flag = <code class="lang-kotlin">--strand</code> Default = <a href="../../org.veupathdb.lib.cli.diamond.opts/-query-strand/-both/index.html">QueryStrand.Both</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/swipe.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/swipe.html
deleted file mode 100644
index 0aaad928..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/swipe.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>swipe</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/swipe.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/swipe/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">swipe</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>swipe</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="swipe.html">swipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Exhaustive alignment against all database sequences.</p><p class="paragraph">Flag = <code class="lang-kotlin">--swipe</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-exclude.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-exclude.html
deleted file mode 100644
index e469af61..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-exclude.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>taxonExclude</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-exclude.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/taxonExclude/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">taxonExclude</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>taxon</span><wbr></wbr><span><span>Exclude</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="taxon-exclude.html">taxonExclude</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><p class="paragraph">Exclude list of taxon ids.</p><p class="paragraph">TODO: comma separated list on serialization!</p><p class="paragraph">Flag = <code class="lang-kotlin">--taxon-exclude</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-list.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-list.html
deleted file mode 100644
index bae10549..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-list.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>taxonList</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/taxon-list.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/taxonList/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">taxonList</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>taxon</span><wbr></wbr><span><span>List</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="taxon-list.html">taxonList</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><p class="paragraph">Restrict search to list of taxon ids.</p><p class="paragraph">Flag = <code class="lang-kotlin">--taxonlist</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unal.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unal.html
deleted file mode 100644
index a8759d25..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unal.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>unal</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unal.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/unal/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">unal</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>unal</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unal.html">unal</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Report unaligned queries.</p><p class="paragraph">Flag = <code class="lang-kotlin">--unal</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file-format.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file-format.html
deleted file mode 100644
index b688c0ad..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file-format.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>unalignedFileFormat</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file-format.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/unalignedFileFormat/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">unalignedFileFormat</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>unaligned</span><wbr></wbr><span>File</span><wbr></wbr><span><span>Format</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unaligned-file-format.html">unalignedFileFormat</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-query-file-format/index.html">QueryFileFormat</a></div><p class="paragraph">Format of unaligned query file.</p><p class="paragraph">Flag = <code class="lang-kotlin">--unfmt</code> Default = <a href="../../org.veupathdb.lib.cli.diamond.opts/-query-file-format/-f-a-s-t-a/index.html">QueryFileFormat.FASTA</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file.html
deleted file mode 100644
index 8d418864..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>unalignedFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/unaligned-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerGeneralOptionContainerImpl/unalignedFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">unalignedFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>unaligned</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="unaligned-file.html">unalignedFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">File for unaligned queries.</p><p class="paragraph">Flag = <code class="lang-kotlin">--un</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/-aligner-sensitivity-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/-aligner-sensitivity-option-container-impl.html
deleted file mode 100644
index 2719500e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/-aligner-sensitivity-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerSensitivityOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/-aligner-sensitivity-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerSensitivityOptionContainerImpl/AlignerSensitivityOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerSensitivityOptionContainerImpl</a><span class="delimiter">/</span><span class="current">AlignerSensitivityOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Sensitivity</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/index.html
deleted file mode 100644
index 8133a9cb..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/index.html
+++ /dev/null
@@ -1,259 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerSensitivityOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerSensitivityOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">AlignerSensitivityOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Sensitivity</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">AlignerSensitivityOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-aligner-sensitivity-option-container/index.html">AlignerSensitivityOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="358877423%2FConstructors%2F769193423" anchor-label="AlignerSensitivityOptionContainerImpl" id="358877423%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-sensitivity-option-container-impl.html"><span>Aligner</span><wbr></wbr><span>Sensitivity</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="358877423%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="-161954046%2FProperties%2F769193423" anchor-label="fast" id="-161954046%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="../../org.veupathdb.lib.cli.diamond.opts/-aligner-sensitivity-option-container/fast.html"><span><span>fast</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-161954046%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
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-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerSensitivityOptionContainerImpl/shapes/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerSensitivityOptionContainerImpl</a><span class="delimiter">/</span><span class="current">shapes</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>shapes</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="shapes.html">shapes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/-aligner-view-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/-aligner-view-option-container-impl.html
deleted file mode 100644
index f4e17e7d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/-aligner-view-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerViewOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/-aligner-view-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerViewOptionContainerImpl/AlignerViewOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerViewOptionContainerImpl</a><span class="delimiter">/</span><span class="current">AlignerViewOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>View</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/index.html
deleted file mode 100644
index 9afdbca4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/index.html
+++ /dev/null
@@ -1,139 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>AlignerViewOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    } else {
-        const savedDarkMode = JSON.parse(storage)
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerViewOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">AlignerViewOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Aligner</span><wbr></wbr><span>View</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">AlignerViewOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-aligner-view-option-container/index.html">AlignerViewOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="815444623%2FConstructors%2F769193423" anchor-label="AlignerViewOptionContainerImpl" id="815444623%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-view-option-container-impl.html"><span>Aligner</span><wbr></wbr><span>View</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="815444623%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="430369773%2FProperties%2F769193423" anchor-label="maxTargetSeqs" id="430369773%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="max-target-seqs.html"><span>max</span><wbr></wbr><span>Target</span><wbr></wbr><span><span>Seqs</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="430369773%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-target-seqs.html">maxTargetSeqs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Maximum number of target sequences to report alignments for.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="779460865%2FProperties%2F769193423" anchor-label="top" id="779460865%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="top.html"><span><span>top</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="779460865%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="top.html">top</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Report alignments within this percentage range of top alignment score.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/max-target-seqs.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/max-target-seqs.html
deleted file mode 100644
index f4e3e653..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/max-target-seqs.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>maxTargetSeqs</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/max-target-seqs.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerViewOptionContainerImpl/maxTargetSeqs/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">AlignerViewOptionContainerImpl</a><span class="delimiter">/</span><span class="current">maxTargetSeqs</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>max</span><wbr></wbr><span>Target</span><wbr></wbr><span><span>Seqs</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-target-seqs.html">maxTargetSeqs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Maximum number of target sequences to report alignments for.</p><p class="paragraph">Flag = <code class="lang-kotlin">--max-target-seqs</code> | <code class="lang-kotlin">-k</code> Default = <code class="lang-kotlin">25</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/top.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/top.html
deleted file mode 100644
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/top.html
+++ /dev/null
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-<head>
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-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/top.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-                <div class="sidebar--inner" id="sideMenu"></div>
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-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/AlignerViewOptionContainerImpl/top/#/PointingToDeclaration//769193423">
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/-clustering-general-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/-clustering-general-option-container-impl.html
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/-clustering-general-option-container-impl.html
+++ /dev/null
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-<!DOCTYPE html>
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-        <div id="container">
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/cluster-steps.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/cluster-steps.html
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/cluster-steps.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
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-            <div class="library-name">
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-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringGeneralOptionContainerImpl/clusterSteps/#/PointingToDeclaration//769193423">
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-  <div class="cover ">
-    <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Steps</span></span></h1>
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-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-steps.html">clusterSteps</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><p class="paragraph">Clustering steps.</p><p class="paragraph">Flag = <code class="lang-kotlin">--cluster-steps</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/index.html
deleted file mode 100644
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/index.html
+++ /dev/null
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-<!DOCTYPE html>
-<html class="no-js">
-<head>
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-<link href="../../../styles/style.css" rel="Stylesheet">
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-            <div class="library-name">
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-            <div id="main">
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-    <h1 class="cover"><span>Clustering</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-clustering-general-option-container-impl.html"><span>Clustering</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-232807889%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="-348574290%2FProperties%2F769193423" anchor-label="clusterSteps" id="-348574290%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cluster-steps.html"><span>cluster</span><wbr></wbr><span><span>Steps</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-348574290%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-steps.html">clusterSteps</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Clustering steps.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="73007000%2FProperties%2F769193423" anchor-label="kmerRanking" id="73007000%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="kmer-ranking.html"><span>kmer</span><wbr></wbr><span><span>Ranking</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="73007000%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="kmer-ranking.html">kmerRanking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Rank sequences based on kmer frequency in linear stage.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-207559716%2FProperties%2F769193423" anchor-label="roundApproxID" id="-207559716%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="round-approx-i-d.html"><span>round</span><wbr></wbr><span>Approx</span><wbr></wbr><span><span>ID</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-207559716%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="round-approx-i-d.html">roundApproxID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Per-round approx-id cutoffs for cascaded clustering.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1451505655%2FProperties%2F769193423" anchor-label="roundCoverage" id="-1451505655%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="round-coverage.html"><span>round</span><wbr></wbr><span><span>Coverage</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1451505655%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="round-coverage.html">roundCoverage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><div class="brief "><p class="paragraph">Per-round coverage cutoffs for cascaded clustering.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/kmer-ranking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/kmer-ranking.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>kmerRanking</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
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-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/kmer-ranking.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringGeneralOptionContainerImpl/kmerRanking/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">kmerRanking</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>kmer</span><wbr></wbr><span><span>Ranking</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="kmer-ranking.html">kmerRanking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Rank sequences based on kmer frequency in linear stage.</p><p class="paragraph">Flag = <code class="lang-kotlin">--kmer-ranking</code> Default = `` Type = <code class="lang-kotlin">bool</code> Config Var = <code class="lang-kotlin">kmer_ranking</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/round-approx-i-d.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/round-approx-i-d.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>roundApproxID</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/round-approx-i-d.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringGeneralOptionContainerImpl/roundApproxID/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">roundApproxID</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>round</span><wbr></wbr><span>Approx</span><wbr></wbr><span><span>ID</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="round-approx-i-d.html">roundApproxID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><p class="paragraph">Per-round approx-id cutoffs for cascaded clustering.</p><p class="paragraph">Flag = <code class="lang-kotlin">--round-approx-id</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/round-coverage.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/round-coverage.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>roundCoverage</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/round-coverage.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
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-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringGeneralOptionContainerImpl/roundCoverage/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringGeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">roundCoverage</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>round</span><wbr></wbr><span><span>Coverage</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="round-coverage.html">roundCoverage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.collections/-list/index.html">List</a><span class="token operator">&lt;</span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a><span class="token operator">&gt;</span></div><p class="paragraph">Per-round coverage cutoffs for cascaded clustering.</p><p class="paragraph">Flag = <code class="lang-kotlin">--round-coverage</code></p></div></div>
-</div>
-      <div class="footer">
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-                class="pull-right"><span>Generated by </span><a
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-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/-clustering-input-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/-clustering-input-option-container-impl.html
deleted file mode 100644
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/-clustering-input-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
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-                <div class="sidebar--inner" id="sideMenu"></div>
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-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringInputOptionContainerImpl/ClusteringInputOptionContainerImpl/#/PointingToDeclaration//769193423">
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-  <div class="cover ">
-    <h1 class="cover"><span>Clustering</span><wbr></wbr><span>Input</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
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-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
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-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/clusters-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/clusters-file.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>clustersFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
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-    <div class="navigation--inner">
-        <div class="navigation-title">
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-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/clusters-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringInputOptionContainerImpl/clustersFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringInputOptionContainerImpl</a><span class="delimiter">/</span><span class="current">clustersFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>clusters</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="clusters-file.html">clustersFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Clustering input file as 2-column tabular format mapping sequences to representatives.</p><p class="paragraph">Flag = <code class="lang-kotlin">--clusters</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-input-option-container-impl/index.html
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+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ClusteringInputOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
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-<link href="../../../styles/style.css" rel="Stylesheet">
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-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
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-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-            </div>
-            <div class="library-version">
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-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
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-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringInputOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">ClusteringInputOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Clustering</span><wbr></wbr><span>Input</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">ClusteringInputOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-clustering-input-option-container/index.html">ClusteringInputOptionContainer</a></div></div></div>
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-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="-1161207121%2FConstructors%2F769193423" anchor-label="ClusteringInputOptionContainerImpl" id="-1161207121%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-              <div class=""><span class="inline-flex">
-                  <div><a href="-clustering-input-option-container-impl.html"><span>Clustering</span><wbr></wbr><span>Input</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1161207121%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="1790792388%2FProperties%2F769193423" anchor-label="clustersFile" id="1790792388%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="clusters-file.html"><span>clusters</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1790792388%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="clusters-file.html">clustersFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Clustering input file as 2-column tabular format mapping sequences to representatives.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/-clustering-reassign-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/-clustering-reassign-option-container-impl.html
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-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ClusteringReassignOptionContainerImpl</title>
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-            <div class="library-name">
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-                            diamondcli
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-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringReassignOptionContainerImpl/ClusteringReassignOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringReassignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">ClusteringReassignOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Clustering</span><wbr></wbr><span>Reassign</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
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-</div>
-      <div class="footer">
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-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
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-    </div>
-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/index.html
deleted file mode 100644
index ca0e153c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/index.html
+++ /dev/null
@@ -1,154 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ClusteringReassignOptionContainerImpl</title>
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-    <script>var pathToRoot = "../../../";</script>
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-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
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-                            diamondcli
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-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringReassignOptionContainerImpl///PointingToDeclaration//769193423">
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-  <div class="cover ">
-    <h1 class="cover"><span>Clustering</span><wbr></wbr><span>Reassign</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">ClusteringReassignOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-clustering-reassign-option-container/index.html">ClusteringReassignOptionContainer</a></div></div></div>
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-                <div class="title">
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-            <div class="main-subrow keyValue ">
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-                  <div><a href="member-cover.html"><span>member</span><wbr></wbr><span><span>Cover</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1125425966%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="member-cover.html">memberCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum coverage percentage of the cluster member sequence.</p></div></div></div>
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-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
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-                <div class="title">
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-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mutual-cover.html">mutualCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Minimum mutual coverage percentage of the cluster member and representative sequence.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/member-cover.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/member-cover.html
deleted file mode 100644
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>memberCover</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
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-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
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-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/member-cover.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringReassignOptionContainerImpl/memberCover/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringReassignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">memberCover</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>member</span><wbr></wbr><span><span>Cover</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="member-cover.html">memberCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum coverage percentage of the cluster member sequence.</p><p class="paragraph">Flag = <code class="lang-kotlin">--member-cover</code> Default = <code class="lang-kotlin">80.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
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-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/memory-limit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/memory-limit.html
deleted file mode 100644
index 8f704d6b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/memory-limit.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>memoryLimit</title>
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-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
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-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
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-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
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-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/memory-limit.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringReassignOptionContainerImpl/memoryLimit/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringReassignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">memoryLimit</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>memory</span><wbr></wbr><span><span>Limit</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="memory-limit.html">memoryLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Memory limit in GB</p><p class="paragraph">Flag = <code class="lang-kotlin">--memory-limit</code> | <code class="lang-kotlin">-M</code> Default = <code class="lang-kotlin">&quot;16G&quot;</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/mutual-cover.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/mutual-cover.html
deleted file mode 100644
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/mutual-cover.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mutualCover</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-    } else {
-        const savedDarkMode = JSON.parse(storage)
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
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-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-clustering-reassign-option-container-impl/mutual-cover.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/ClusteringReassignOptionContainerImpl/mutualCover/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">ClusteringReassignOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mutualCover</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mutual</span><wbr></wbr><span><span>Cover</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mutual-cover.html">mutualCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Minimum mutual coverage percentage of the cluster member and representative sequence.</p><p class="paragraph">Flag = <code class="lang-kotlin">--mutual-cover</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/-general-d-b-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/-general-d-b-option-container-impl.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>GeneralDBOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/-general-d-b-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralDBOptionContainerImpl/GeneralDBOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralDBOptionContainerImpl</a><span class="delimiter">/</span><span class="current">GeneralDBOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>DBOption</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/database-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/database-file.html
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+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>databaseFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
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-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/database-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralDBOptionContainerImpl/databaseFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralDBOptionContainerImpl</a><span class="delimiter">/</span><span class="current">databaseFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>database</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="database-file.html">databaseFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Path to the target DIAMOND database file.</p><p class="paragraph">Flag = <code class="lang-kotlin">--db</code> | <code class="lang-kotlin">-d</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/index.html
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+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>GeneralDBOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
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-</head>
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-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
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-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-            <div class="sidebar" id="leftColumn">
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-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralDBOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">GeneralDBOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>DBOption</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">GeneralDBOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-general-d-b-option-container/index.html">GeneralDBOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="-604102929%2FConstructors%2F769193423" anchor-label="GeneralDBOptionContainerImpl" id="-604102929%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-d-b-option-container-impl.html"><span>General</span><wbr></wbr><span>DBOption</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-604102929%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
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-        <div class="table"><a data-name="-1806941922%2FProperties%2F769193423" anchor-label="databaseFile" id="-1806941922%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="database-file.html"><span>database</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1806941922%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="database-file.html">databaseFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Path to the target DIAMOND database file.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/-general-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/-general-option-container-impl.html
deleted file mode 100644
index 294510e4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/-general-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
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-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOptionContainerImpl/GeneralOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">GeneralOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/index.html
deleted file mode 100644
index b7181ba8..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/index.html
+++ /dev/null
@@ -1,184 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>GeneralOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
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-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">GeneralOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">GeneralOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-general-option-container/index.html">GeneralOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="733450223%2FConstructors%2F769193423" anchor-label="GeneralOptionContainerImpl" id="733450223%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-option-container-impl.html"><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="733450223%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="1587632163%2FProperties%2F769193423" anchor-label="log" id="1587632163%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="log.html"><span><span>log</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1587632163%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log.html">log</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Enable even more verbose terminal output, which is also written to a file named <code class="lang-kotlin">diamond.log</code> is the current working directory.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1554259789%2FProperties%2F769193423" anchor-label="quiet" id="-1554259789%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="quiet.html"><span><span>quiet</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1554259789%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="quiet.html">quiet</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Disable all terminal output.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1808025618%2FProperties%2F769193423" anchor-label="tempDir" id="-1808025618%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="temp-dir.html"><span>temp</span><wbr></wbr><span><span>Dir</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1808025618%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="temp-dir.html">tempDir</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Directory for temporary files.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="987262558%2FProperties%2F769193423" anchor-label="threads" id="987262558%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="threads.html"><span><span>threads</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="987262558%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="threads.html">threads</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Number of CPU threads.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-35995995%2FProperties%2F769193423" anchor-label="verbose" id="-35995995%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="verbose.html"><span><span>verbose</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-35995995%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="verbose.html">verbose</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Enable more verbose terminal output.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/log.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/log.html
deleted file mode 100644
index 0e2c9e7b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/log.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>log</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/log.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOptionContainerImpl/log/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">log</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>log</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log.html">log</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Enable even more verbose terminal output, which is also written to a file named <code class="lang-kotlin">diamond.log</code> is the current working directory.</p><blockquote class="quotation"><p class="paragraph"><code class="lang-kotlin">--log</code></p></blockquote><p class="paragraph">Default: <code class="lang-kotlin">false</code></p><p class="paragraph">TODO: how does this interact with <a href="quiet.html">quiet</a> and <a href="verbose.html">verbose</a>?</p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/quiet.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/quiet.html
deleted file mode 100644
index d73059cc..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/quiet.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>quiet</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/quiet.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOptionContainerImpl/quiet/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">quiet</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>quiet</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="quiet.html">quiet</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Disable all terminal output.</p><blockquote class="quotation"><p class="paragraph"><code class="lang-kotlin">--quiet</code></p></blockquote><p class="paragraph">Default: <code class="lang-kotlin">false</code></p><p class="paragraph">TODO: verify whether this is mutually exclusive with <a href="verbose.html">verbose</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/temp-dir.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/temp-dir.html
deleted file mode 100644
index 9404eea0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/temp-dir.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>tempDir</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/temp-dir.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOptionContainerImpl/tempDir/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">tempDir</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>temp</span><wbr></wbr><span><span>Dir</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="temp-dir.html">tempDir</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Directory for temporary files.</p><blockquote class="quotation"><p class="paragraph"><code class="lang-kotlin">--tmpdir/-t &lt;path&gt;</code></p></blockquote><p class="paragraph">Default: <code class="lang-kotlin">null</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/threads.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/threads.html
deleted file mode 100644
index ee31eb81..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/threads.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>threads</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/threads.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOptionContainerImpl/threads/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">threads</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>threads</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="threads.html">threads</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Number of CPU threads.</p><p class="paragraph">By default, the program will auto-detect and use all available virtual cores on the machine.</p><blockquote class="quotation"><p class="paragraph"><code class="lang-kotlin">--threads/-p #</code></p></blockquote><p class="paragraph">Setting this to a value that is less than or equal to zero results in the option being omitted from the CLI call.</p><p class="paragraph">Default: <code class="lang-kotlin">0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/verbose.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/verbose.html
deleted file mode 100644
index 014529cd..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/verbose.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>verbose</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/verbose.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOptionContainerImpl/verbose/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOptionContainerImpl</a><span class="delimiter">/</span><span class="current">verbose</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>verbose</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="verbose.html">verbose</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Enable more verbose terminal output.</p><blockquote class="quotation"><p class="paragraph"><code class="lang-kotlin">--verbose/-v</code></p></blockquote><p class="paragraph">Default: <code class="lang-kotlin">false</code></p><p class="paragraph">TODO: verify whether this is mutually exclusive with <a href="quiet.html">quiet</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/-general-output-header-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/-general-output-header-option-container-impl.html
deleted file mode 100644
index 29cd562c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/-general-output-header-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>GeneralOutputHeaderOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/-general-output-header-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOutputHeaderOptionContainerImpl/GeneralOutputHeaderOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOutputHeaderOptionContainerImpl</a><span class="delimiter">/</span><span class="current">GeneralOutputHeaderOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Header</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/header.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/header.html
deleted file mode 100644
index 2daf1f67..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/header.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>header</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/header.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOutputHeaderOptionContainerImpl/header/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOutputHeaderOptionContainerImpl</a><span class="delimiter">/</span><span class="current">header</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>header</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="header.html">header</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-header-option/index.html">HeaderOption</a></div><p class="paragraph">Use header lines in tabular output format.</p><ul><li><p class="paragraph">Flag: <code class="lang-kotlin">--header</code></p></li><li><p class="paragraph">Default: <a href="../../org.veupathdb.lib.cli.diamond.opts/-header-option/-none/index.html">HeaderOption.None</a></p></li></ul></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/index.html
deleted file mode 100644
index 69cd782e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/index.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>GeneralOutputHeaderOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOutputHeaderOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">GeneralOutputHeaderOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Header</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">GeneralOutputHeaderOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-general-output-header-option-container/index.html">GeneralOutputHeaderOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="1721971119%2FConstructors%2F769193423" anchor-label="GeneralOutputHeaderOptionContainerImpl" id="1721971119%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-output-header-option-container-impl.html"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Header</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1721971119%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="-2098214120%2FProperties%2F769193423" anchor-label="header" id="-2098214120%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="header.html"><span><span>header</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2098214120%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="header.html">header</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-header-option/index.html">HeaderOption</a></div><div class="brief "><p class="paragraph">Use header lines in tabular output format.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/-general-output-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/-general-output-option-container-impl.html
deleted file mode 100644
index e35cfe21..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/-general-output-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>GeneralOutputOptionContainerImpl</title>
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-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-        if (osDarkSchemePreferred === true) {
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-<link href="../../../styles/style.css" rel="Stylesheet">
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-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/-general-output-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOutputOptionContainerImpl/GeneralOutputOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOutputOptionContainerImpl</a><span class="delimiter">/</span><span class="current">GeneralOutputOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/index.html
deleted file mode 100644
index 018b7e89..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/index.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>GeneralOutputOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
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-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
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-<link href="../../../styles/style.css" rel="Stylesheet">
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-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
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-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
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-    </div>
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-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOutputOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">GeneralOutputOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">GeneralOutputOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-general-output-option-container/index.html">GeneralOutputOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="1712986831%2FConstructors%2F769193423" anchor-label="GeneralOutputOptionContainerImpl" id="1712986831%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-output-option-container-impl.html"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1712986831%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="-2140809003%2FProperties%2F769193423" anchor-label="outputFile" id="-2140809003%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="output-file.html"><span>output</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2140809003%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-file.html">outputFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Path to the output file. If this parameter is omitted, the results will be written to the standard output and all other program output will be suppressed.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
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-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/output-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/output-file.html
deleted file mode 100644
index 3b73c97f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/output-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>outputFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
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-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
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-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/output-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/GeneralOutputOptionContainerImpl/outputFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">GeneralOutputOptionContainerImpl</a><span class="delimiter">/</span><span class="current">outputFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>output</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-file.html">outputFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Path to the output file. If this parameter is omitted, the results will be written to the standard output and all other program output will be suppressed.</p><ul><li><p class="paragraph">Flag = <code class="lang-kotlin">--out</code> | <code class="lang-kotlin">-o</code></p></li></ul></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/-hidden-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/-hidden-option-container-impl.html
deleted file mode 100644
index 6ef22321..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/-hidden-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>HiddenOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/-hidden-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/HiddenOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">HiddenOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Hidden</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/add-self-aln.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/add-self-aln.html
deleted file mode 100644
index 70011a3b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/add-self-aln.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>addSelfAln</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/add-self-aln.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/addSelfAln/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">addSelfAln</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>add</span><wbr></wbr><span>Self</span><wbr></wbr><span><span>Aln</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/aln-out.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/aln-out.html
deleted file mode 100644
index 2d782824..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/aln-out.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>alnOut</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/aln-out.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/alnOut/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">alnOut</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>aln</span><wbr></wbr><span><span>Out</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-score.html
deleted file mode 100644
index a9f0fc1f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-score.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>anchorScore</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-score.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/anchorScore/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">anchorScore</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>anchor</span><wbr></wbr><span><span>Score</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-window.html
deleted file mode 100644
index f19384bb..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-window.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>anchorWindow</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchor-window.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/anchorWindow/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">anchorWindow</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>anchor</span><wbr></wbr><span><span>Window</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">12</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchored-swipe.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchored-swipe.html
deleted file mode 100644
index 1355e492..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchored-swipe.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>anchoredSwipe</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/anchored-swipe.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/anchoredSwipe/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">anchoredSwipe</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>anchored</span><wbr></wbr><span><span>Swipe</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ants.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ants.html
deleted file mode 100644
index 1888eff4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ants.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ants</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ants.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/ants/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">ants</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>ants</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p><p class="paragraph">Default: <code class="lang-kotlin">100</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/approx-backtrace.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/approx-backtrace.html
deleted file mode 100644
index 53a5999b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/approx-backtrace.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>approxBacktrace</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/approx-backtrace.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/approxBacktrace/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">approxBacktrace</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>approx</span><wbr></wbr><span><span>Backtrace</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-cutoff.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-cutoff.html
deleted file mode 100644
index 7dceed0f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-cutoff.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>bCutoff</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-cutoff.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/bCutoff/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">bCutoff</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>b</span><wbr></wbr><span><span>Cutoff</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-match.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-match.html
deleted file mode 100644
index 8ac6bb65..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-match.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>bMatch</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-match.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/bMatch/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">bMatch</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>b</span><wbr></wbr><span><span>Match</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-mismatch.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-mismatch.html
deleted file mode 100644
index 75bb31a8..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-mismatch.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>bMismatch</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/b-mismatch.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/bMismatch/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">bMismatch</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>b</span><wbr></wbr><span><span>Mismatch</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/band-bin.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/band-bin.html
deleted file mode 100644
index dca79b6e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/band-bin.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>bandBin</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/band-bin.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/bandBin/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">bandBin</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>band</span><wbr></wbr><span><span>Bin</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p><p class="paragraph">Default: <code class="lang-kotlin">24</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/bootstrap-block.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/bootstrap-block.html
deleted file mode 100644
index 49fe7236..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/bootstrap-block.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>bootstrapBlock</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/bootstrap-block.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/bootstrapBlock/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">bootstrapBlock</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>bootstrap</span><wbr></wbr><span><span>Block</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p><p class="paragraph">Default: <code class="lang-kotlin">1000000</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-angle.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-angle.html
deleted file mode 100644
index dd472468..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-angle.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cbsAngle</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-angle.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/cbsAngle/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cbsAngle</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cbs</span><wbr></wbr><span><span>Angle</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-err-tolerance.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-err-tolerance.html
deleted file mode 100644
index 8c04b2ed..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-err-tolerance.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cbsErrTolerance</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-err-tolerance.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/cbsErrTolerance/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cbsErrTolerance</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cbs</span><wbr></wbr><span>Err</span><wbr></wbr><span><span>Tolerance</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.00000001</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-it-limit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-it-limit.html
deleted file mode 100644
index 71fc6a9b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-it-limit.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cbsItLimit</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-it-limit.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/cbsItLimit/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cbsItLimit</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cbs</span><wbr></wbr><span>It</span><wbr></wbr><span><span>Limit</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-matrix-scale.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-matrix-scale.html
deleted file mode 100644
index 410f948f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-matrix-scale.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cbsMatrixScale</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-matrix-scale.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/cbsMatrixScale/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cbsMatrixScale</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cbs</span><wbr></wbr><span>Matrix</span><wbr></wbr><span><span>Scale</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p><p class="paragraph">Default: <code class="lang-kotlin">1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-window.html
deleted file mode 100644
index b4ad723b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-window.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cbsWindow</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cbs-window.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/cbsWindow/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cbsWindow</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cbs</span><wbr></wbr><span><span>Window</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">40</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/centroid-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/centroid-factor.html
deleted file mode 100644
index ad7342e9..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/centroid-factor.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>centroidFactor</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/centroid-factor.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/centroidFactor/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">centroidFactor</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>centroid</span><wbr></wbr><span><span>Factor</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">3</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-len-cap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-len-cap.html
deleted file mode 100644
index ba015380..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-len-cap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainingLenCap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-len-cap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/chainingLenCap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainingLenCap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chaining</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Cap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p><p class="paragraph">Default: <code class="lang-kotlin">2.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-gap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-gap.html
deleted file mode 100644
index f4030962..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-gap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainingMaxGap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-gap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/chainingMaxGap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainingMaxGap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chaining</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Gap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-nodes.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-nodes.html
deleted file mode 100644
index caf64fa6..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-nodes.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainingMaxNodes</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-max-nodes.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/chainingMaxNodes/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainingMaxNodes</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chaining</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Nodes</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-min-nodes.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-min-nodes.html
deleted file mode 100644
index c35f5349..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-min-nodes.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainingMinNodes</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-min-nodes.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/chainingMinNodes/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainingMinNodes</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chaining</span><wbr></wbr><span>Min</span><wbr></wbr><span><span>Nodes</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p><p class="paragraph">Default: <code class="lang-kotlin">200</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-range-cover.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-range-cover.html
deleted file mode 100644
index 8e314325..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-range-cover.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainingRangeCover</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-range-cover.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/chainingRangeCover/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainingRangeCover</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chaining</span><wbr></wbr><span>Range</span><wbr></wbr><span><span>Cover</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p><p class="paragraph">Default = <code class="lang-kotlin">8</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-stacked-h-s-p-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-stacked-h-s-p-ratio.html
deleted file mode 100644
index 76762d70..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-stacked-h-s-p-ratio.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chainingStackedHSPRatio</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chaining-stacked-h-s-p-ratio.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/chainingStackedHSPRatio/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chainingStackedHSPRatio</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chaining</span><wbr></wbr><span>Stacked</span><wbr></wbr><span><span>HSPRatio</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chunk-size-multiplier.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chunk-size-multiplier.html
deleted file mode 100644
index 01dfe979..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chunk-size-multiplier.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>chunkSizeMultiplier</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/chunk-size-multiplier.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/chunkSizeMultiplier/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">chunkSizeMultiplier</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>chunk</span><wbr></wbr><span>Size</span><wbr></wbr><span><span>Multiplier</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p><p class="paragraph">Default: <code class="lang-kotlin">4</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/classic-band.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/classic-band.html
deleted file mode 100644
index 92621808..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/classic-band.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>classicBand</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/classic-band.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/classicBand/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">classicBand</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>classic</span><wbr></wbr><span><span>Band</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-algo.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-algo.html
deleted file mode 100644
index 0cbcb1f8..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-algo.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>clusterAlgo</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-algo.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/clusterAlgo/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">clusterAlgo</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Algo</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Clustering algorithm ('mcl')</p><p class="paragraph">TODO: actual values for this enum are dependent on compile flags, it seems     that &quot;cascaded&quot; is the only 'safe' option, &quot;mcl&quot; is dependent on a     compile flag.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-algo</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-graph-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-graph-file.html
deleted file mode 100644
index 73497f43..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-graph-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>clusterGraphFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-graph-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/clusterGraphFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">clusterGraphFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cluster</span><wbr></wbr><span>Graph</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-graph-file</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-restart.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-restart.html
deleted file mode 100644
index 29aad54a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-restart.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>clusterRestart</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-restart.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/clusterRestart/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">clusterRestart</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Restart</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Restart clustering from dumped graph.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-restart</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-similarity.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-similarity.html
deleted file mode 100644
index f3006cc3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-similarity.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>clusterSimilarity</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-similarity.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/clusterSimilarity/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">clusterSimilarity</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Similarity</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Clustering similarity measure.</p><p class="paragraph">TODO: this is some sort of expression string, it's currently unclear what     its rules are.  This should be converted to a complex type for     validation.</p><p class="paragraph">TODO: only seems relevant to <code class="lang-kotlin">cluster</code>, <code class="lang-kotlin">deepclust</code>, <code class="lang-kotlin">linclust</code></p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-similarity</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-threshold.html
deleted file mode 100644
index 9cbc6670..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-threshold.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>clusterThreshold</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cluster-threshold.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/clusterThreshold/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">clusterThreshold</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Threshold</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Threshold for the similarity measure.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/col-bin.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/col-bin.html
deleted file mode 100644
index c5689b37..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/col-bin.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>colBin</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/col-bin.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/colBin/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">colBin</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>col</span><wbr></wbr><span><span>Bin</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p><p class="paragraph">Default: <code class="lang-kotlin">400</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cutoff-score8-bit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cutoff-score8-bit.html
deleted file mode 100644
index 51d83167..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cutoff-score8-bit.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>cutoffScore8Bit</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/cutoff-score8-bit.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/cutoffScore8Bit/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">cutoffScore8Bit</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>cutoff</span><wbr></wbr><span><span>Score8Bit</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p><p class="paragraph">Default: <code class="lang-kotlin">240</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-exp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-exp.html
deleted file mode 100644
index 28e18411..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-exp.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>dExp</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-exp.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/dExp/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">dExp</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>d</span><wbr></wbr><span><span>Exp</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-new.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-new.html
deleted file mode 100644
index 9c624da7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-new.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>dNew</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/d-new.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/dNew/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">dNew</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>d</span><wbr></wbr><span><span>New</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/db-type.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/db-type.html
deleted file mode 100644
index 0024a494..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/db-type.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>dbType</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/db-type.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/dbType/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">dbType</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>db</span><wbr></wbr><span><span>Type</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><p class="paragraph">Type of sequences in database file (nucl/prot).</p><p class="paragraph">Flag: <code class="lang-kotlin">--dbtype</code></p><p class="paragraph">Default: <a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/-amino-acid/index.html">SequenceType.AminoAcid</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/deque-bucket-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/deque-bucket-size.html
deleted file mode 100644
index b56ad95e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/deque-bucket-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>dequeBucketSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/deque-bucket-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/dequeBucketSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">dequeBucketSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>deque</span><wbr></wbr><span>Bucket</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p><p class="paragraph">Default: <code class="lang-kotlin">524288</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-cov.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-cov.html
deleted file mode 100644
index c869be8b..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-cov.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>diagFilterCov</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-cov.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/diagFilterCov/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">diagFilterCov</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>diag</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>Cov</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-i-d.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-i-d.html
deleted file mode 100644
index 87124104..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-i-d.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>diagFilterID</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-filter-i-d.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/diagFilterID/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">diagFilterID</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>diag</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>ID</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-min-estimate.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-min-estimate.html
deleted file mode 100644
index 6086158d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-min-estimate.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>diagMinEstimate</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/diag-min-estimate.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/diagMinEstimate/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">diagMinEstimate</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>diag</span><wbr></wbr><span>Min</span><wbr></wbr><span><span>Estimate</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p><p class="paragraph">Default: <code class="lang-kotlin">17</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ext-yield.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ext-yield.html
deleted file mode 100644
index 3881adeb..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ext-yield.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>extYield</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ext-yield.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/extYield/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">extYield</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>ext</span><wbr></wbr><span><span>Yield</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-cap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-cap.html
deleted file mode 100644
index 1e253605..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-cap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>familyCap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-cap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/familyCap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">familyCap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>family</span><wbr></wbr><span><span>Cap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-counts-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-counts-file.html
deleted file mode 100644
index 434d4c03..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-counts-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>familyCountsFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/family-counts-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/familyCountsFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">familyCountsFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>family</span><wbr></wbr><span>Counts</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fast-tsv.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fast-tsv.html
deleted file mode 100644
index 87b76c85..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fast-tsv.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>fastTsv</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fast-tsv.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/fastTsv/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">fastTsv</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>fast</span><wbr></wbr><span><span>Tsv</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fetch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fetch-size.html
deleted file mode 100644
index 12f436f1..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fetch-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>fetchSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/fetch-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/fetchSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">fetchSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>fetch</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Trace point fetch size.</p><p class="paragraph">Flag: <code class="lang-kotlin">--fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">4096u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file1.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file1.html
deleted file mode 100644
index 4f4d4dff..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file1.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>file1</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file1.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/file1/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">file1</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>file1</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file2.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file2.html
deleted file mode 100644
index 00d899a4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file2.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>file2</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/file2.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/file2/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">file2</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>file2</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/freq-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/freq-threshold.html
deleted file mode 100644
index 92a305ce..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/freq-threshold.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>freqThreshold</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/freq-threshold.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/freqThreshold/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">freqThreshold</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>freq</span><wbr></wbr><span><span>Threshold</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/full-sw-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/full-sw-len.html
deleted file mode 100644
index 48a3ea8a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/full-sw-len.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>fullSwLen</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/full-sw-len.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/fullSwLen/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">fullSwLen</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>full</span><wbr></wbr><span>Sw</span><wbr></wbr><span><span>Len</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-diag-bit-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-diag-bit-score.html
deleted file mode 100644
index 92e77026..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-diag-bit-score.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>gappedFilterDiagBitScore</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-diag-bit-score.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/gappedFilterDiagBitScore/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">gappedFilterDiagBitScore</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span>Diag</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p><p class="paragraph">Default: <code class="lang-kotlin">12.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-e-value1.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-e-value1.html
deleted file mode 100644
index 105e0c10..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-e-value1.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>gappedFilterEValue1</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-e-value1.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/gappedFilterEValue1/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">gappedFilterEValue1</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>EValue1</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-window.html
deleted file mode 100644
index 0f03205c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-window.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>gappedFilterWindow</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/gapped-filter-window.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/gappedFilterWindow/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">gappedFilterWindow</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>Window</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">200</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/graph-algo.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/graph-algo.html
deleted file mode 100644
index c6399ce3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/graph-algo.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>graphAlgo</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/graph-algo.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/graphAlgo/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">graphAlgo</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>graph</span><wbr></wbr><span><span>Algo</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p><p class="paragraph">Default: <a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/-greedy-vortex-cover/index.html">GraphAlgorithm.GreedyVortexCover</a></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hamming-ext.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hamming-ext.html
deleted file mode 100644
index 8f2f339c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hamming-ext.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>hammingExt</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hamming-ext.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/hammingExt/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">hammingExt</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>hamming</span><wbr></wbr><span><span>Ext</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hard-masked.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hard-masked.html
deleted file mode 100644
index 053b26d0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hard-masked.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>hardMasked</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hard-masked.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/hardMasked/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">hardMasked</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>hard</span><wbr></wbr><span><span>Masked</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hash-join-swap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hash-join-swap.html
deleted file mode 100644
index 7195632a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hash-join-swap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>hashJoinSwap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/hash-join-swap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/hashJoinSwap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">hashJoinSwap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>hash</span><wbr></wbr><span>Join</span><wbr></wbr><span><span>Swap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-left.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-left.html
deleted file mode 100644
index 0c2551fb..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-left.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>idLeft</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-left.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/idLeft/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">idLeft</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>id</span><wbr></wbr><span><span>Left</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-n.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-n.html
deleted file mode 100644
index db19c9c9..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-n.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>idN</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-n.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/idN/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">idN</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>id</span><wbr></wbr><span><span>N</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-right.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-right.html
deleted file mode 100644
index 1ffd7cb3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-right.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>idRight</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/id-right.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/idRight/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">idRight</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>id</span><wbr></wbr><span><span>Right</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/index.html
deleted file mode 100644
index 62d1a4d5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/index.html
+++ /dev/null
@@ -1,2584 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>HiddenOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">HiddenOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Hidden</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">HiddenOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html">HiddenOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="-2095629207%2FConstructors%2F769193423" anchor-label="HiddenOptionContainerImpl" id="-2095629207%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-hidden-option-container-impl.html"><span>Hidden</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2095629207%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="-1096391847%2FProperties%2F769193423" anchor-label="addSelfAln" id="-1096391847%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="add-self-aln.html"><span>add</span><wbr></wbr><span>Self</span><wbr></wbr><span><span>Aln</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1096391847%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="375625252%2FProperties%2F769193423" anchor-label="alnOut" id="375625252%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="aln-out.html"><span>aln</span><wbr></wbr><span><span>Out</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="375625252%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-498281979%2FProperties%2F769193423" anchor-label="anchoredSwipe" id="-498281979%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="anchored-swipe.html"><span>anchored</span><wbr></wbr><span><span>Swipe</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-498281979%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1786965518%2FProperties%2F769193423" anchor-label="anchorScore" id="1786965518%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="anchor-score.html"><span>anchor</span><wbr></wbr><span><span>Score</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1786965518%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1967732342%2FProperties%2F769193423" anchor-label="anchorWindow" id="-1967732342%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="anchor-window.html"><span>anchor</span><wbr></wbr><span><span>Window</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1967732342%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1661679875%2FProperties%2F769193423" anchor-label="ants" id="1661679875%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ants.html"><span><span>ants</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1661679875%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2041244679%2FProperties%2F769193423" anchor-label="approxBacktrace" id="2041244679%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="approx-backtrace.html"><span>approx</span><wbr></wbr><span><span>Backtrace</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2041244679%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1614223111%2FProperties%2F769193423" anchor-label="bandBin" id="-1614223111%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="band-bin.html"><span>band</span><wbr></wbr><span><span>Bin</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1614223111%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1614342972%2FProperties%2F769193423" anchor-label="bCutoff" id="1614342972%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="b-cutoff.html"><span>b</span><wbr></wbr><span><span>Cutoff</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1614342972%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1381500596%2FProperties%2F769193423" anchor-label="bMatch" id="-1381500596%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="b-match.html"><span>b</span><wbr></wbr><span><span>Match</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1381500596%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="107966843%2FProperties%2F769193423" anchor-label="bMismatch" id="107966843%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="b-mismatch.html"><span>b</span><wbr></wbr><span><span>Mismatch</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="107966843%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1932009104%2FProperties%2F769193423" anchor-label="bootstrapBlock" id="1932009104%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="bootstrap-block.html"><span>bootstrap</span><wbr></wbr><span><span>Block</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1932009104%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1187228272%2FProperties%2F769193423" anchor-label="cbsAngle" id="-1187228272%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cbs-angle.html"><span>cbs</span><wbr></wbr><span><span>Angle</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1187228272%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1036675441%2FProperties%2F769193423" anchor-label="cbsErrTolerance" id="-1036675441%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cbs-err-tolerance.html"><span>cbs</span><wbr></wbr><span>Err</span><wbr></wbr><span><span>Tolerance</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1036675441%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2098603469%2FProperties%2F769193423" anchor-label="cbsItLimit" id="-2098603469%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cbs-it-limit.html"><span>cbs</span><wbr></wbr><span>It</span><wbr></wbr><span><span>Limit</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2098603469%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-159696742%2FProperties%2F769193423" anchor-label="cbsMatrixScale" id="-159696742%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cbs-matrix-scale.html"><span>cbs</span><wbr></wbr><span>Matrix</span><wbr></wbr><span><span>Scale</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-159696742%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1937921863%2FProperties%2F769193423" anchor-label="cbsWindow" id="1937921863%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cbs-window.html"><span>cbs</span><wbr></wbr><span><span>Window</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1937921863%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1836659680%2FProperties%2F769193423" anchor-label="centroidFactor" id="-1836659680%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="centroid-factor.html"><span>centroid</span><wbr></wbr><span><span>Factor</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1836659680%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1000766511%2FProperties%2F769193423" anchor-label="chainingLenCap" id="-1000766511%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chaining-len-cap.html"><span>chaining</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Cap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1000766511%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="921872412%2FProperties%2F769193423" anchor-label="chainingMaxGap" id="921872412%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chaining-max-gap.html"><span>chaining</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Gap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="921872412%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-886450335%2FProperties%2F769193423" anchor-label="chainingMaxNodes" id="-886450335%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chaining-max-nodes.html"><span>chaining</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Nodes</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-886450335%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="999556047%2FProperties%2F769193423" anchor-label="chainingMinNodes" id="999556047%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chaining-min-nodes.html"><span>chaining</span><wbr></wbr><span>Min</span><wbr></wbr><span><span>Nodes</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="999556047%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="468374260%2FProperties%2F769193423" anchor-label="chainingRangeCover" id="468374260%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chaining-range-cover.html"><span>chaining</span><wbr></wbr><span>Range</span><wbr></wbr><span><span>Cover</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="468374260%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1489062913%2FProperties%2F769193423" anchor-label="chainingStackedHSPRatio" id="-1489062913%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chaining-stacked-h-s-p-ratio.html"><span>chaining</span><wbr></wbr><span>Stacked</span><wbr></wbr><span><span>HSPRatio</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1489062913%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1599055036%2FProperties%2F769193423" anchor-label="chunkSizeMultiplier" id="1599055036%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="chunk-size-multiplier.html"><span>chunk</span><wbr></wbr><span>Size</span><wbr></wbr><span><span>Multiplier</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1599055036%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2094639172%2FProperties%2F769193423" anchor-label="classicBand" id="2094639172%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="classic-band.html"><span>classic</span><wbr></wbr><span><span>Band</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2094639172%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="885698942%2FProperties%2F769193423" anchor-label="clusterAlgo" id="885698942%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cluster-algo.html"><span>cluster</span><wbr></wbr><span><span>Algo</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="885698942%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1834706655%2FProperties%2F769193423" anchor-label="clusterGraphFile" id="1834706655%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cluster-graph-file.html"><span>cluster</span><wbr></wbr><span>Graph</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1834706655%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1215667366%2FProperties%2F769193423" anchor-label="clusterRestart" id="-1215667366%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cluster-restart.html"><span>cluster</span><wbr></wbr><span><span>Restart</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1215667366%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-498081810%2FProperties%2F769193423" anchor-label="clusterSimilarity" id="-498081810%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cluster-similarity.html"><span>cluster</span><wbr></wbr><span><span>Similarity</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-498081810%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-372033154%2FProperties%2F769193423" anchor-label="clusterThreshold" id="-372033154%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cluster-threshold.html"><span>cluster</span><wbr></wbr><span><span>Threshold</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-372033154%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-99007256%2FProperties%2F769193423" anchor-label="colBin" id="-99007256%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="col-bin.html"><span>col</span><wbr></wbr><span><span>Bin</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-99007256%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-246504271%2FProperties%2F769193423" anchor-label="cutoffScore8Bit" id="-246504271%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="cutoff-score8-bit.html"><span>cutoff</span><wbr></wbr><span><span>Score8Bit</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-246504271%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1681655959%2FProperties%2F769193423" anchor-label="dbType" id="1681655959%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="db-type.html"><span>db</span><wbr></wbr><span><span>Type</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1681655959%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="db-type.html">dbType</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-716671008%2FProperties%2F769193423" anchor-label="dequeBucketSize" id="-716671008%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="deque-bucket-size.html"><span>deque</span><wbr></wbr><span>Bucket</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-716671008%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="758710774%2FProperties%2F769193423" anchor-label="dExp" id="758710774%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="d-exp.html"><span>d</span><wbr></wbr><span><span>Exp</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="758710774%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1971090716%2FProperties%2F769193423" anchor-label="diagFilterCov" id="-1971090716%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="diag-filter-cov.html"><span>diag</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>Cov</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1971090716%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="439397265%2FProperties%2F769193423" anchor-label="diagFilterID" id="439397265%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="diag-filter-i-d.html"><span>diag</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>ID</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="439397265%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-229674244%2FProperties%2F769193423" anchor-label="diagMinEstimate" id="-229674244%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="diag-min-estimate.html"><span>diag</span><wbr></wbr><span>Min</span><wbr></wbr><span><span>Estimate</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-229674244%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1887390675%2FProperties%2F769193423" anchor-label="dNew" id="1887390675%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="d-new.html"><span>d</span><wbr></wbr><span><span>New</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1887390675%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-601927293%2FProperties%2F769193423" anchor-label="extYield" id="-601927293%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ext-yield.html"><span>ext</span><wbr></wbr><span><span>Yield</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-601927293%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2107036227%2FProperties%2F769193423" anchor-label="familyCap" id="-2107036227%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="family-cap.html"><span>family</span><wbr></wbr><span><span>Cap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2107036227%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="563537163%2FProperties%2F769193423" anchor-label="familyCountsFile" id="563537163%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="family-counts-file.html"><span>family</span><wbr></wbr><span>Counts</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="563537163%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1819324464%2FProperties%2F769193423" anchor-label="fastTsv" id="-1819324464%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="fast-tsv.html"><span>fast</span><wbr></wbr><span><span>Tsv</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1819324464%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-726549936%2FProperties%2F769193423" anchor-label="fetchSize" id="-726549936%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="fetch-size.html"><span>fetch</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-726549936%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1837653558%2FProperties%2F769193423" anchor-label="file1" id="1837653558%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="file1.html"><span><span>file1</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1837653558%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1868673365%2FProperties%2F769193423" anchor-label="file2" id="1868673365%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="file2.html"><span><span>file2</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1868673365%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1477770408%2FProperties%2F769193423" anchor-label="freqThreshold" id="-1477770408%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="freq-threshold.html"><span>freq</span><wbr></wbr><span><span>Threshold</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1477770408%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="54282825%2FProperties%2F769193423" anchor-label="fullSwLen" id="54282825%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="full-sw-len.html"><span>full</span><wbr></wbr><span>Sw</span><wbr></wbr><span><span>Len</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="54282825%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1173994226%2FProperties%2F769193423" anchor-label="gappedFilterDiagBitScore" id="-1173994226%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="gapped-filter-diag-bit-score.html"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span>Diag</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1173994226%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-6725705%2FProperties%2F769193423" anchor-label="gappedFilterEValue1" id="-6725705%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="gapped-filter-e-value1.html"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>EValue1</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-6725705%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2027329554%2FProperties%2F769193423" anchor-label="gappedFilterWindow" id="-2027329554%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="gapped-filter-window.html"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>Window</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2027329554%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="642874922%2FProperties%2F769193423" anchor-label="graphAlgo" id="642874922%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="graph-algo.html"><span>graph</span><wbr></wbr><span><span>Algo</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="642874922%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="354788343%2FProperties%2F769193423" anchor-label="hammingExt" id="354788343%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="hamming-ext.html"><span>hamming</span><wbr></wbr><span><span>Ext</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="354788343%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1097084711%2FProperties%2F769193423" anchor-label="hardMasked" id="-1097084711%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="hard-masked.html"><span>hard</span><wbr></wbr><span><span>Masked</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1097084711%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1571260860%2FProperties%2F769193423" anchor-label="hashJoinSwap" id="-1571260860%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="hash-join-swap.html"><span>hash</span><wbr></wbr><span>Join</span><wbr></wbr><span><span>Swap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1571260860%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1847670547%2FProperties%2F769193423" anchor-label="idLeft" id="-1847670547%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="id-left.html"><span>id</span><wbr></wbr><span><span>Left</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1847670547%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-498994408%2FProperties%2F769193423" anchor-label="idN" id="-498994408%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="id-n.html"><span>id</span><wbr></wbr><span><span>N</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-498994408%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-209804118%2FProperties%2F769193423" anchor-label="idRight" id="-209804118%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="id-right.html"><span>id</span><wbr></wbr><span><span>Right</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-209804118%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="984794090%2FProperties%2F769193423" anchor-label="joinHTFactor" id="984794090%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="join-h-t-factor.html"><span>join</span><wbr></wbr><span><span>HTFactor</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="984794090%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="409375909%2FProperties%2F769193423" anchor-label="joinSplitKeyLen" id="409375909%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="join-split-key-len.html"><span>join</span><wbr></wbr><span>Split</span><wbr></wbr><span>Key</span><wbr></wbr><span><span>Len</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="409375909%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2136037818%2FProperties%2F769193423" anchor-label="joinSplitSize" id="2136037818%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="join-split-size.html"><span>join</span><wbr></wbr><span>Split</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2136037818%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="792206492%2FProperties%2F769193423" anchor-label="key2" id="792206492%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="key2.html"><span><span>key2</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="792206492%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1209408448%2FProperties%2F769193423" anchor-label="leftMostInterval" id="1209408448%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="left-most-interval.html"><span>left</span><wbr></wbr><span>Most</span><wbr></wbr><span><span>Interval</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1209408448%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1535618935%2FProperties%2F769193423" anchor-label="lengthRatioThreshold" id="-1535618935%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="length-ratio-threshold.html"><span>length</span><wbr></wbr><span>Ratio</span><wbr></wbr><span><span>Threshold</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1535618935%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1784096216%2FProperties%2F769193423" anchor-label="loadBalancing" id="1784096216%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="load-balancing.html"><span>load</span><wbr></wbr><span><span>Balancing</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1784096216%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1185945075%2FProperties%2F769193423" anchor-label="logExtend" id="-1185945075%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="log-extend.html"><span>log</span><wbr></wbr><span><span>Extend</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1185945075%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-594240885%2FProperties%2F769193423" anchor-label="logQuery" id="-594240885%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="log-query.html"><span>log</span><wbr></wbr><span><span>Query</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-594240885%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="361498919%2FProperties%2F769193423" anchor-label="logSubject" id="361498919%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="log-subject.html"><span>log</span><wbr></wbr><span><span>Subject</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="361498919%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1457904257%2FProperties%2F769193423" anchor-label="mapAny" id="-1457904257%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="map-any.html"><span>map</span><wbr></wbr><span><span>Any</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1457904257%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-544778686%2FProperties%2F769193423" anchor-label="maxCells" id="-544778686%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="max-cells.html"><span>max</span><wbr></wbr><span><span>Cells</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-544778686%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1559176796%2FProperties%2F769193423" anchor-label="maximumSeedFrequency" id="-1559176796%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="maximum-seed-frequency.html"><span>maximum</span><wbr></wbr><span>Seed</span><wbr></wbr><span><span>Frequency</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1559176796%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1133511993%2FProperties%2F769193423" anchor-label="maxIndirection" id="1133511993%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="max-indirection.html"><span>max</span><wbr></wbr><span><span>Indirection</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1133511993%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1373382177%2FProperties%2F769193423" anchor-label="maxMotifLen" id="1373382177%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="max-motif-len.html"><span>max</span><wbr></wbr><span>Motif</span><wbr></wbr><span><span>Len</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1373382177%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1372662707%2FProperties%2F769193423" anchor-label="maxSwipeDp" id="-1372662707%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="max-swipe-dp.html"><span>max</span><wbr></wbr><span>Swipe</span><wbr></wbr><span><span>Dp</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1372662707%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mcl-chunk-size.html"><span>mcl</span><wbr></wbr><span>Chunk</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-139556649%2FProperties%2F769193423"></span>
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-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1557212486%2FProperties%2F769193423" anchor-label="mclExpansion" id="1557212486%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mcl-expansion.html"><span>mcl</span><wbr></wbr><span><span>Expansion</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1557212486%2FProperties%2F769193423"></span>
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-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="462171963%2FProperties%2F769193423" anchor-label="mclInflation" id="462171963%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mcl-inflation.html"><span>mcl</span><wbr></wbr><span><span>Inflation</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="462171963%2FProperties%2F769193423"></span>
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-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="376046763%2FProperties%2F769193423" anchor-label="mclMaxIterations" id="376046763%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mcl-max-iterations.html"><span>mcl</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Iterations</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="376046763%2FProperties%2F769193423"></span>
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-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-28662357%2FProperties%2F769193423" anchor-label="mclNonSymmetric" id="-28662357%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-              <div class=""><span class="inline-flex">
-                  <div><a href="mcl-non-symmetric.html"><span>mcl</span><wbr></wbr><span>Non</span><wbr></wbr><span><span>Symmetric</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-28662357%2FProperties%2F769193423"></span>
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-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="17121720%2FProperties%2F769193423" anchor-label="mclSparsitySwitch" id="17121720%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
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-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mcl-sparsity-switch.html"><span>mcl</span><wbr></wbr><span>Sparsity</span><wbr></wbr><span><span>Switch</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="17121720%2FProperties%2F769193423"></span>
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-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-586889882%2FProperties%2F769193423" anchor-label="mclStats" id="-586889882%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="mcl-stats.html"><span>mcl</span><wbr></wbr><span><span>Stats</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-586889882%2FProperties%2F769193423"></span>
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-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1344044642%2FProperties%2F769193423" anchor-label="memoryIntervals" id="-1344044642%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="memory-intervals.html"><span>memory</span><wbr></wbr><span><span>Intervals</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1344044642%2FProperties%2F769193423"></span>
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-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="942558671%2FProperties%2F769193423" anchor-label="minBandOverlap" id="942558671%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="min-band-overlap.html"><span>min</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Overlap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="942558671%2FProperties%2F769193423"></span>
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-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1394660135%2FProperties%2F769193423" anchor-label="minimizerWindow" id="1394660135%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="minimizer-window.html"><span>minimizer</span><wbr></wbr><span><span>Window</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1394660135%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2115409437%2FProperties%2F769193423" anchor-label="minLenRatio" id="-2115409437%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="min-len-ratio.html"><span>min</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Ratio</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2115409437%2FProperties%2F769193423"></span>
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-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2099547959%2FProperties%2F769193423" anchor-label="minRealignOverhang" id="-2099547959%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="min-realign-overhang.html"><span>min</span><wbr></wbr><span>Realign</span><wbr></wbr><span><span>Overhang</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2099547959%2FProperties%2F769193423"></span>
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-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-138047254%2FProperties%2F769193423" anchor-label="minTaskTracePts" id="-138047254%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="min-task-trace-pts.html"><span>min</span><wbr></wbr><span>Task</span><wbr></wbr><span>Trace</span><wbr></wbr><span><span>Pts</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-138047254%2FProperties%2F769193423"></span>
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-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1441317548%2FProperties%2F769193423" anchor-label="motifMaskFile" id="-1441317548%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="motif-mask-file.html"><span>motif</span><wbr></wbr><span>Mask</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1441317548%2FProperties%2F769193423"></span>
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-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1751575505%2FProperties%2F769193423" anchor-label="narrowBandCov" id="1751575505%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="narrow-band-cov.html"><span>narrow</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Cov</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1751575505%2FProperties%2F769193423"></span>
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-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1381232080%2FProperties%2F769193423" anchor-label="narrowBandFactor" id="-1381232080%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="narrow-band-factor.html"><span>narrow</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Factor</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1381232080%2FProperties%2F769193423"></span>
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-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="118787623%2FProperties%2F769193423" anchor-label="neighborhoodScore" id="118787623%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="neighborhood-score.html"><span>neighborhood</span><wbr></wbr><span><span>Score</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="118787623%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1758538966%2FProperties%2F769193423" anchor-label="neighbors" id="-1758538966%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="neighbors.html"><span><span>neighbors</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1758538966%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-830177406%2FProperties%2F769193423" anchor-label="no8BitExtension" id="-830177406%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no8-bit-extension.html"><span>no8Bit</span><wbr></wbr><span><span>Extension</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-830177406%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-740223385%2FProperties%2F769193423" anchor-label="noChainingMergeHSPs" id="-740223385%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-chaining-merge-h-s-ps.html"><span>no</span><wbr></wbr><span>Chaining</span><wbr></wbr><span>Merge</span><wbr></wbr><span><span>HSPs</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-740223385%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-827860680%2FProperties%2F769193423" anchor-label="noDict" id="-827860680%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-dict.html"><span>no</span><wbr></wbr><span><span>Dict</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-827860680%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1803073955%2FProperties%2F769193423" anchor-label="noForwardFp" id="-1803073955%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-forward-fp.html"><span>no</span><wbr></wbr><span>Forward</span><wbr></wbr><span><span>Fp</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1803073955%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="525494988%2FProperties%2F769193423" anchor-label="noLogFile" id="525494988%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-log-file.html"><span>no</span><wbr></wbr><span>Log</span><wbr></wbr><span><span>File</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="525494988%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-633386687%2FProperties%2F769193423" anchor-label="noReextend" id="-633386687%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-reextend.html"><span>no</span><wbr></wbr><span><span>Reextend</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-633386687%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="272538475%2FProperties%2F769193423" anchor-label="noRefMasking" id="272538475%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-ref-masking.html"><span>no</span><wbr></wbr><span>Ref</span><wbr></wbr><span><span>Masking</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="272538475%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1899583761%2FProperties%2F769193423" anchor-label="noReorder" id="1899583761%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-reorder.html"><span>no</span><wbr></wbr><span><span>Reorder</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1899583761%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="849977878%2FProperties%2F769193423" anchor-label="noSwipeRealign" id="849977878%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="no-swipe-realign.html"><span>no</span><wbr></wbr><span>Swipe</span><wbr></wbr><span><span>Realign</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="849977878%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1130431171%2FProperties%2F769193423" anchor-label="oidList" id="1130431171%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="oid-list.html"><span>oid</span><wbr></wbr><span><span>List</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1130431171%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-576396636%2FProperties%2F769193423" anchor-label="outputFp" id="-576396636%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="output-fp.html"><span>output</span><wbr></wbr><span><span>Fp</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-576396636%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1449834322%2FProperties%2F769193423" anchor-label="outputHits" id="-1449834322%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="output-hits.html"><span>output</span><wbr></wbr><span><span>Hits</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1449834322%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="672831386%2FProperties%2F769193423" anchor-label="pAlign" id="672831386%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="p-align.html"><span>p</span><wbr></wbr><span><span>Align</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="672831386%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2010092861%2FProperties%2F769193423" anchor-label="pathCutoff" id="2010092861%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="path-cutoff.html"><span>path</span><wbr></wbr><span><span>Cutoff</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2010092861%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="833862359%2FProperties%2F769193423" anchor-label="pBest" id="833862359%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="p-best.html"><span>p</span><wbr></wbr><span><span>Best</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="833862359%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1757700881%2FProperties%2F769193423" anchor-label="pipelineShort" id="1757700881%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="pipeline-short.html"><span>pipeline</span><wbr></wbr><span><span>Short</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1757700881%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2036904928%2FProperties%2F769193423" anchor-label="prefixScan" id="-2036904928%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="prefix-scan.html"><span>prefix</span><wbr></wbr><span><span>Scan</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2036904928%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1719360984%2FProperties%2F769193423" anchor-label="queryCount" id="-1719360984%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="query-count.html"><span>query</span><wbr></wbr><span><span>Count</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1719360984%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-933450030%2FProperties%2F769193423" anchor-label="queryMatchDistanceThreshold" id="-933450030%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="query-match-distance-threshold.html"><span>query</span><wbr></wbr><span>Match</span><wbr></wbr><span>Distance</span><wbr></wbr><span><span>Threshold</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-933450030%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-41182078%2FProperties%2F769193423" anchor-label="queryMemory" id="-41182078%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="query-memory.html"><span>query</span><wbr></wbr><span><span>Memory</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-41182078%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1011260447%2FProperties%2F769193423" anchor-label="radixBits" id="-1011260447%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="radix-bits.html"><span>radix</span><wbr></wbr><span><span>Bits</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1011260447%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1093830598%2FProperties%2F769193423" anchor-label="radixClusterBuffered" id="-1093830598%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="radix-cluster-buffered.html"><span>radix</span><wbr></wbr><span>Cluster</span><wbr></wbr><span><span>Buffered</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1093830598%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="739299636%2FProperties%2F769193423" anchor-label="rankFactor" id="739299636%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="rank-factor.html"><span>rank</span><wbr></wbr><span><span>Factor</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="739299636%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-774879901%2FProperties%2F769193423" anchor-label="rankingCutoffBitScore" id="-774879901%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ranking-cutoff-bit-score.html"><span>ranking</span><wbr></wbr><span>Cutoff</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-774879901%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1325511307%2FProperties%2F769193423" anchor-label="rankingScoreDropFactor" id="-1325511307%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ranking-score-drop-factor.html"><span>ranking</span><wbr></wbr><span>Score</span><wbr></wbr><span>Drop</span><wbr></wbr><span><span>Factor</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1325511307%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-109685981%2FProperties%2F769193423" anchor-label="raw" id="-109685981%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="raw.html"><span><span>raw</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-109685981%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="76987753%2FProperties%2F769193423" anchor-label="reassignMax" id="76987753%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="reassign-max.html"><span>reassign</span><wbr></wbr><span><span>Max</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="76987753%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="907070438%2FProperties%2F769193423" anchor-label="reassignOverlap" id="907070438%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="reassign-overlap.html"><span>reassign</span><wbr></wbr><span><span>Overlap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="907070438%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-523425630%2FProperties%2F769193423" anchor-label="reassignRatio" id="-523425630%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="reassign-ratio.html"><span>reassign</span><wbr></wbr><span><span>Ratio</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-523425630%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="204694593%2FProperties%2F769193423" anchor-label="relaxedEValueFactor" id="204694593%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="relaxed-e-value-factor.html"><span>relaxed</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Factor</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="204694593%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="477256418%2FProperties%2F769193423" anchor-label="resume" id="477256418%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="resume.html"><span><span>resume</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="477256418%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-119707991%2FProperties%2F769193423" anchor-label="reverse" id="-119707991%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="reverse.html"><span><span>reverse</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-119707991%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2078486386%2FProperties%2F769193423" anchor-label="rho" id="2078486386%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="rho.html"><span><span>rho</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2078486386%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="2120459938%2FProperties%2F769193423" anchor-label="scoreEstimateFactor" id="2120459938%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="score-estimate-factor.html"><span>score</span><wbr></wbr><span>Estimate</span><wbr></wbr><span><span>Factor</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="2120459938%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="307404534%2FProperties%2F769193423" anchor-label="scoreRatio" id="307404534%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="score-ratio.html"><span>score</span><wbr></wbr><span><span>Ratio</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="307404534%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="975821833%2FProperties%2F769193423" anchor-label="seedHitDensity" id="975821833%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="seed-hit-density.html"><span>seed</span><wbr></wbr><span>Hit</span><wbr></wbr><span><span>Density</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="975821833%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-144282298%2FProperties%2F769193423" anchor-label="seedWeight" id="-144282298%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="seed-weight.html"><span>seed</span><wbr></wbr><span><span>Weight</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-144282298%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-255964893%2FProperties%2F769193423" anchor-label="self" id="-255964893%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="self.html"><span><span>self</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-255964893%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="976481202%2FProperties%2F769193423" anchor-label="shortQueryMaxLen" id="976481202%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="short-query-max-len.html"><span>short</span><wbr></wbr><span>Query</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Len</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="976481202%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1329469684%2FProperties%2F769193423" anchor-label="shortQueryUngappedBitScore" id="-1329469684%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="short-query-ungapped-bit-score.html"><span>short</span><wbr></wbr><span>Query</span><wbr></wbr><span>Ungapped</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1329469684%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1935208534%2FProperties%2F769193423" anchor-label="shortSeqIDs" id="1935208534%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="short-seq-i-ds.html"><span>short</span><wbr></wbr><span>Seq</span><wbr></wbr><span><span>IDs</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1935208534%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-175197851%2FProperties%2F769193423" anchor-label="simpleFreq" id="-175197851%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="simple-freq.html"><span>simple</span><wbr></wbr><span><span>Freq</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-175197851%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="651437122%2FProperties%2F769193423" anchor-label="sketchSize" id="651437122%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="sketch-size.html"><span>sketch</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="651437122%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1431990521%2FProperties%2F769193423" anchor-label="sortJoin" id="-1431990521%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="sort-join.html"><span>sort</span><wbr></wbr><span><span>Join</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1431990521%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1934108244%2FProperties%2F769193423" anchor-label="spacePenalty" id="-1934108244%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="space-penalty.html"><span>space</span><wbr></wbr><span><span>Penalty</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1934108244%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1358677555%2FProperties%2F769193423" anchor-label="storeQueryQuality" id="1358677555%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="store-query-quality.html"><span>store</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Quality</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1358677555%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1041391520%2FProperties%2F769193423" anchor-label="strictGVC" id="-1041391520%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="strict-g-v-c.html"><span>strict</span><wbr></wbr><span><span>GVC</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1041391520%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1080178755%2FProperties%2F769193423" anchor-label="superblock" id="-1080178755%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="superblock.html"><span><span>superblock</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1080178755%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1436366075%2FProperties%2F769193423" anchor-label="swipeChunkSize" id="1436366075%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="swipe-chunk-size.html"><span>swipe</span><wbr></wbr><span>Chunk</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1436366075%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-809550773%2FProperties%2F769193423" anchor-label="swipeTaskSize" id="-809550773%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="swipe-task-size.html"><span>swipe</span><wbr></wbr><span>Task</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-809550773%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="582124025%2FProperties%2F769193423" anchor-label="tantanMaxRepeatOffset" id="582124025%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="tantan-max-repeat-offset.html"><span>tantan</span><wbr></wbr><span>Max</span><wbr></wbr><span>Repeat</span><wbr></wbr><span><span>Offset</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="582124025%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2104545827%2FProperties%2F769193423" anchor-label="tantanUngapped" id="-2104545827%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="tantan-ungapped.html"><span>tantan</span><wbr></wbr><span><span>Ungapped</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2104545827%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1736187707%2FProperties%2F769193423" anchor-label="targetBias" id="-1736187707%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="target-bias.html"><span>target</span><wbr></wbr><span><span>Bias</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1736187707%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-499039935%2FProperties%2F769193423" anchor-label="targetFetchSize" id="-499039935%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="target-fetch-size.html"><span>target</span><wbr></wbr><span>Fetch</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-499039935%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1854852469%2FProperties%2F769193423" anchor-label="targetHardCap" id="1854852469%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="target-hard-cap.html"><span>target</span><wbr></wbr><span>Hard</span><wbr></wbr><span><span>Cap</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1854852469%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-613052424%2FProperties%2F769193423" anchor-label="targetParallelVerbosity" id="-613052424%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="target-parallel-verbosity.html"><span>target</span><wbr></wbr><span>Parallel</span><wbr></wbr><span><span>Verbosity</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-613052424%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-59762432%2FProperties%2F769193423" anchor-label="tileSize" id="-59762432%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="tile-size.html"><span>tile</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-59762432%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="314173706%2FProperties%2F769193423" anchor-label="timeout" id="314173706%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="timeout.html"><span><span>timeout</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="314173706%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-917696899%2FProperties%2F769193423" anchor-label="tracePtFetchSize" id="-917696899%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="trace-pt-fetch-size.html"><span>trace</span><wbr></wbr><span>Pt</span><wbr></wbr><span>Fetch</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-917696899%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1675215900%2FProperties%2F769193423" anchor-label="transcriptLenEstimate" id="-1675215900%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="transcript-len-estimate.html"><span>transcript</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Estimate</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1675215900%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1046821615%2FProperties%2F769193423" anchor-label="tree" id="-1046821615%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="tree.html"><span><span>tree</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1046821615%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1392185763%2FProperties%2F769193423" anchor-label="tsvReadSize" id="-1392185763%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="tsv-read-size.html"><span>tsv</span><wbr></wbr><span>Read</span><wbr></wbr><span><span>Size</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1392185763%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-842157835%2FProperties%2F769193423" anchor-label="type" id="-842157835%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="type.html"><span><span>type</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-842157835%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1196946127%2FProperties%2F769193423" anchor-label="ungappedEValue" id="-1196946127%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ungapped-e-value.html"><span>ungapped</span><wbr></wbr><span><span>EValue</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1196946127%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2022126099%2FProperties%2F769193423" anchor-label="ungappedEValueShort" id="-2022126099%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ungapped-e-value-short.html"><span>ungapped</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Short</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2022126099%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1715555891%2FProperties%2F769193423" anchor-label="ungappedWindow" id="-1715555891%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="ungapped-window.html"><span>ungapped</span><wbr></wbr><span><span>Window</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1715555891%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-863160027%2FProperties%2F769193423" anchor-label="upGmaDist" id="-863160027%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="up-gma-dist.html"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span><span>Dist</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-863160027%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2037193231%2FProperties%2F769193423" anchor-label="upGmaEdgeLimit" id="-2037193231%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="up-gma-edge-limit.html"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span>Edge</span><wbr></wbr><span><span>Limit</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2037193231%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1562063013%2FProperties%2F769193423" anchor-label="upGmaInput" id="1562063013%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="up-gma-input.html"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span><span>Input</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1562063013%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="880400098%2FProperties%2F769193423" anchor-label="useDatasetField" id="880400098%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="use-dataset-field.html"><span>use</span><wbr></wbr><span>Dataset</span><wbr></wbr><span><span>Field</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="880400098%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1900068112%2FProperties%2F769193423" anchor-label="useSmithWaterman" id="1900068112%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="use-smith-waterman.html"><span>use</span><wbr></wbr><span>Smith</span><wbr></wbr><span><span>Waterman</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1900068112%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1019848238%2FProperties%2F769193423" anchor-label="weightedGVC" id="1019848238%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="weighted-g-v-c.html"><span>weighted</span><wbr></wbr><span><span>GVC</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1019848238%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-h-t-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-h-t-factor.html
deleted file mode 100644
index 59da7b66..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-h-t-factor.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>joinHTFactor</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-h-t-factor.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/joinHTFactor/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">joinHTFactor</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>join</span><wbr></wbr><span><span>HTFactor</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.3</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-key-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-key-len.html
deleted file mode 100644
index dfd221ab..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-key-len.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>joinSplitKeyLen</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-key-len.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/joinSplitKeyLen/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">joinSplitKeyLen</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>join</span><wbr></wbr><span>Split</span><wbr></wbr><span>Key</span><wbr></wbr><span><span>Len</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">17u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-size.html
deleted file mode 100644
index 3f37db26..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>joinSplitSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/join-split-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/joinSplitSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">joinSplitSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>join</span><wbr></wbr><span>Split</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">100000u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/key2.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/key2.html
deleted file mode 100644
index 786f03e3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/key2.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>key2</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/key2.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/key2/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">key2</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>key2</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/left-most-interval.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/left-most-interval.html
deleted file mode 100644
index b65a4eb0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/left-most-interval.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>leftMostInterval</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/left-most-interval.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/leftMostInterval/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">leftMostInterval</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>left</span><wbr></wbr><span>Most</span><wbr></wbr><span><span>Interval</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p><p class="paragraph">Default: <code class="lang-kotlin">32</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/length-ratio-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/length-ratio-threshold.html
deleted file mode 100644
index bd8f77ba..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/length-ratio-threshold.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>lengthRatioThreshold</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/length-ratio-threshold.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/lengthRatioThreshold/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">lengthRatioThreshold</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>length</span><wbr></wbr><span>Ratio</span><wbr></wbr><span><span>Threshold</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/load-balancing.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/load-balancing.html
deleted file mode 100644
index bfb98e3f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/load-balancing.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>loadBalancing</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/load-balancing.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/loadBalancing/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">loadBalancing</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>load</span><wbr></wbr><span><span>Balancing</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-extend.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-extend.html
deleted file mode 100644
index 7958abbe..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-extend.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>logExtend</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-extend.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/logExtend/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">logExtend</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>log</span><wbr></wbr><span><span>Extend</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-query.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-query.html
deleted file mode 100644
index 466fddb6..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-query.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>logQuery</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-query.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/logQuery/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">logQuery</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>log</span><wbr></wbr><span><span>Query</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-subject.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-subject.html
deleted file mode 100644
index 6b146915..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-subject.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>logSubject</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/log-subject.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/logSubject/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">logSubject</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>log</span><wbr></wbr><span><span>Subject</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/map-any.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/map-any.html
deleted file mode 100644
index 5a7a815f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/map-any.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mapAny</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/map-any.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mapAny/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mapAny</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>map</span><wbr></wbr><span><span>Any</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-cells.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-cells.html
deleted file mode 100644
index 9976da5f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-cells.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>maxCells</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-cells.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/maxCells/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">maxCells</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>max</span><wbr></wbr><span><span>Cells</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p><p class="paragraph">Default: <code class="lang-kotlin">10000000u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-indirection.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-indirection.html
deleted file mode 100644
index 7fc21023..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-indirection.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>maxIndirection</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-indirection.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/maxIndirection/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">maxIndirection</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>max</span><wbr></wbr><span><span>Indirection</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-motif-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-motif-len.html
deleted file mode 100644
index 4a192dd4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-motif-len.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>maxMotifLen</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-motif-len.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/maxMotifLen/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">maxMotifLen</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>max</span><wbr></wbr><span>Motif</span><wbr></wbr><span><span>Len</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">30</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-swipe-dp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-swipe-dp.html
deleted file mode 100644
index ad1968f8..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-swipe-dp.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>maxSwipeDp</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/max-swipe-dp.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/maxSwipeDp/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">maxSwipeDp</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>max</span><wbr></wbr><span>Swipe</span><wbr></wbr><span><span>Dp</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p><p class="paragraph">Default: <code class="lang-kotlin">1000000</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/maximum-seed-frequency.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/maximum-seed-frequency.html
deleted file mode 100644
index 9aebd5ee..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/maximum-seed-frequency.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>maximumSeedFrequency</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/maximum-seed-frequency.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/maximumSeedFrequency/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">maximumSeedFrequency</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>maximum</span><wbr></wbr><span>Seed</span><wbr></wbr><span><span>Frequency</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Maximum seed frequency.</p><p class="paragraph">Flag: <code class="lang-kotlin">--seed-freq</code></p><p class="paragraph">Default = <code class="lang-kotlin">-15.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-chunk-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-chunk-size.html
deleted file mode 100644
index 8b56742f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-chunk-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mclChunkSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-chunk-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mclChunkSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mclChunkSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mcl</span><wbr></wbr><span>Chunk</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL chunk size per thread.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-chunk-size</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-expansion.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-expansion.html
deleted file mode 100644
index 45541451..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-expansion.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mclExpansion</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-expansion.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mclExpansion/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mclExpansion</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mcl</span><wbr></wbr><span><span>Expansion</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL expansion coefficient.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-expansion</code></p><p class="paragraph">Default: <code class="lang-kotlin">2</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-inflation.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-inflation.html
deleted file mode 100644
index ba6588d0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-inflation.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mclInflation</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-inflation.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mclInflation/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mclInflation</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mcl</span><wbr></wbr><span><span>Inflation</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">MCL inflation coefficient.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-inflation</code></p><p class="paragraph">Default: <code class="lang-kotlin">2.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-max-iterations.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-max-iterations.html
deleted file mode 100644
index 5ab779c7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-max-iterations.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mclMaxIterations</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-max-iterations.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mclMaxIterations/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mclMaxIterations</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mcl</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Iterations</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL maximum iterations.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-max-iterations</code></p><p class="paragraph">Default: <code class="lang-kotlin">100</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-non-symmetric.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-non-symmetric.html
deleted file mode 100644
index ffa504c7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-non-symmetric.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mclNonSymmetric</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-non-symmetric.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mclNonSymmetric/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mclNonSymmetric</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mcl</span><wbr></wbr><span>Non</span><wbr></wbr><span><span>Symmetric</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-nonsymmetric</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-sparsity-switch.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-sparsity-switch.html
deleted file mode 100644
index 9ca750c7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-sparsity-switch.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mclSparsitySwitch</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-sparsity-switch.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mclSparsitySwitch/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mclSparsitySwitch</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mcl</span><wbr></wbr><span>Sparsity</span><wbr></wbr><span><span>Switch</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">MCL switch to sparse matrix computation.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-sparsity-switch</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.8</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-stats.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-stats.html
deleted file mode 100644
index d234a207..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-stats.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>mclStats</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/mcl-stats.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/mclStats/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">mclStats</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>mcl</span><wbr></wbr><span><span>Stats</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Some stats about the connected components in MCL.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-stats</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/memory-intervals.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/memory-intervals.html
deleted file mode 100644
index e32f8126..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/memory-intervals.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>memoryIntervals</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/memory-intervals.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/memoryIntervals/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">memoryIntervals</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>memory</span><wbr></wbr><span><span>Intervals</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p><p class="paragraph">Default: <code class="lang-kotlin">2</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-band-overlap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-band-overlap.html
deleted file mode 100644
index 3db5700f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-band-overlap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minBandOverlap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-band-overlap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/minBandOverlap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minBandOverlap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>min</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Overlap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-len-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-len-ratio.html
deleted file mode 100644
index 8cba0c6a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-len-ratio.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minLenRatio</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-len-ratio.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/minLenRatio/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minLenRatio</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>min</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Ratio</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-realign-overhang.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-realign-overhang.html
deleted file mode 100644
index e7b714af..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-realign-overhang.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minRealignOverhang</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-realign-overhang.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/minRealignOverhang/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minRealignOverhang</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>min</span><wbr></wbr><span>Realign</span><wbr></wbr><span><span>Overhang</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p><p class="paragraph">Default: <code class="lang-kotlin">30</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-task-trace-pts.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-task-trace-pts.html
deleted file mode 100644
index be094d15..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-task-trace-pts.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minTaskTracePts</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/min-task-trace-pts.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/minTaskTracePts/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minTaskTracePts</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>min</span><wbr></wbr><span>Task</span><wbr></wbr><span>Trace</span><wbr></wbr><span><span>Pts</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p><p class="paragraph">Default: <code class="lang-kotlin">1024</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/minimizer-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/minimizer-window.html
deleted file mode 100644
index ebb635f1..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/minimizer-window.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>minimizerWindow</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/minimizer-window.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/minimizerWindow/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">minimizerWindow</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>minimizer</span><wbr></wbr><span><span>Window</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/motif-mask-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/motif-mask-file.html
deleted file mode 100644
index 2964c4c1..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/motif-mask-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>motifMaskFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/motif-mask-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/motifMaskFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">motifMaskFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>motif</span><wbr></wbr><span>Mask</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--motif-mask-file</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-cov.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-cov.html
deleted file mode 100644
index 13b60ef9..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-cov.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>narrowBandCov</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-cov.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/narrowBandCov/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">narrowBandCov</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>narrow</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Cov</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-factor.html
deleted file mode 100644
index a9c1b8d0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-factor.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>narrowBandFactor</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/narrow-band-factor.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/narrowBandFactor/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">narrowBandFactor</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>narrow</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Factor</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighborhood-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighborhood-score.html
deleted file mode 100644
index 623a99d1..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighborhood-score.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>neighborhoodScore</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighborhood-score.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/neighborhoodScore/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">neighborhoodScore</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>neighborhood</span><wbr></wbr><span><span>Score</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighbors.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighbors.html
deleted file mode 100644
index 520d126c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighbors.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>neighbors</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/neighbors.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/neighbors/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">neighbors</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>neighbors</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--neighbors</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-chaining-merge-h-s-ps.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-chaining-merge-h-s-ps.html
deleted file mode 100644
index cf1aa826..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-chaining-merge-h-s-ps.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noChainingMergeHSPs</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-chaining-merge-h-s-ps.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noChainingMergeHSPs/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noChainingMergeHSPs</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Chaining</span><wbr></wbr><span>Merge</span><wbr></wbr><span><span>HSPs</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-dict.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-dict.html
deleted file mode 100644
index 3cb5bd0d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-dict.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noDict</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-dict.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noDict/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noDict</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span><span>Dict</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-forward-fp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-forward-fp.html
deleted file mode 100644
index c6f0d92e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-forward-fp.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noForwardFp</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-forward-fp.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noForwardFp/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noForwardFp</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Forward</span><wbr></wbr><span><span>Fp</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-log-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-log-file.html
deleted file mode 100644
index 29329fa9..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-log-file.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noLogFile</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-log-file.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noLogFile/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noLogFile</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Log</span><wbr></wbr><span><span>File</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reextend.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reextend.html
deleted file mode 100644
index ab1f82d5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reextend.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noReextend</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reextend.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noReextend/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noReextend</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span><span>Reextend</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-ref-masking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-ref-masking.html
deleted file mode 100644
index 91c0a754..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-ref-masking.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noRefMasking</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-ref-masking.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noRefMasking/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noRefMasking</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Ref</span><wbr></wbr><span><span>Masking</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reorder.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reorder.html
deleted file mode 100644
index 2f5909de..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reorder.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noReorder</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-reorder.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noReorder/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noReorder</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span><span>Reorder</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-swipe-realign.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-swipe-realign.html
deleted file mode 100644
index 7ff2037d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-swipe-realign.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>noSwipeRealign</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no-swipe-realign.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/noSwipeRealign/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">noSwipeRealign</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no</span><wbr></wbr><span>Swipe</span><wbr></wbr><span><span>Realign</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no8-bit-extension.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no8-bit-extension.html
deleted file mode 100644
index 89d9df54..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no8-bit-extension.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>no8BitExtension</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/no8-bit-extension.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/no8BitExtension/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">no8BitExtension</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>no8Bit</span><wbr></wbr><span><span>Extension</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/oid-list.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/oid-list.html
deleted file mode 100644
index 38131327..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/oid-list.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>oidList</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/oid-list.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/oidList/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">oidList</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>oid</span><wbr></wbr><span><span>List</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-fp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-fp.html
deleted file mode 100644
index 3968b788..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-fp.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>outputFp</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-fp.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/outputFp/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">outputFp</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>output</span><wbr></wbr><span><span>Fp</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-hits.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-hits.html
deleted file mode 100644
index c3d1a09c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-hits.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>outputHits</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/output-hits.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/outputHits/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">outputHits</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>output</span><wbr></wbr><span><span>Hits</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-align.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-align.html
deleted file mode 100644
index 6e4eb9af..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-align.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>pAlign</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-align.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/pAlign/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">pAlign</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>p</span><wbr></wbr><span><span>Align</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-best.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-best.html
deleted file mode 100644
index 5030c64a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-best.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>pBest</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/p-best.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/pBest/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">pBest</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>p</span><wbr></wbr><span><span>Best</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.05</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/path-cutoff.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/path-cutoff.html
deleted file mode 100644
index 743f27e2..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/path-cutoff.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>pathCutoff</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/path-cutoff.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/pathCutoff/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">pathCutoff</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>path</span><wbr></wbr><span><span>Cutoff</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.92</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/pipeline-short.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/pipeline-short.html
deleted file mode 100644
index 76b4a254..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/pipeline-short.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>pipelineShort</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/pipeline-short.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/pipelineShort/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">pipelineShort</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>pipeline</span><wbr></wbr><span><span>Short</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/prefix-scan.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/prefix-scan.html
deleted file mode 100644
index ed4f5bf7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/prefix-scan.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>prefixScan</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/prefix-scan.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/prefixScan/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">prefixScan</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>prefix</span><wbr></wbr><span><span>Scan</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-count.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-count.html
deleted file mode 100644
index 4501a13f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-count.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>queryCount</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-count.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/queryCount/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">queryCount</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>query</span><wbr></wbr><span><span>Count</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p><p class="paragraph">Default: <code class="lang-kotlin">1</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-match-distance-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-match-distance-threshold.html
deleted file mode 100644
index d61c00d9..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-match-distance-threshold.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>queryMatchDistanceThreshold</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-match-distance-threshold.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/queryMatchDistanceThreshold/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">queryMatchDistanceThreshold</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>query</span><wbr></wbr><span>Match</span><wbr></wbr><span>Distance</span><wbr></wbr><span><span>Threshold</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-memory.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-memory.html
deleted file mode 100644
index 2c404b8e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-memory.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>queryMemory</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/query-memory.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/queryMemory/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">queryMemory</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>query</span><wbr></wbr><span><span>Memory</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-bits.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-bits.html
deleted file mode 100644
index a548d332..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-bits.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>radixBits</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-bits.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/radixBits/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">radixBits</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>radix</span><wbr></wbr><span><span>Bits</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p><p class="paragraph">Default: <code class="lang-kotlin">8u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-cluster-buffered.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-cluster-buffered.html
deleted file mode 100644
index eb8783c6..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-cluster-buffered.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>radixClusterBuffered</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/radix-cluster-buffered.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/radixClusterBuffered/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">radixClusterBuffered</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>radix</span><wbr></wbr><span>Cluster</span><wbr></wbr><span><span>Buffered</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rank-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rank-factor.html
deleted file mode 100644
index 5d5e53ff..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rank-factor.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>rankFactor</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rank-factor.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/rankFactor/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">rankFactor</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>rank</span><wbr></wbr><span><span>Factor</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-cutoff-bit-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-cutoff-bit-score.html
deleted file mode 100644
index c7511747..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-cutoff-bit-score.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>rankingCutoffBitScore</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-cutoff-bit-score.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/rankingCutoffBitScore/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">rankingCutoffBitScore</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>ranking</span><wbr></wbr><span>Cutoff</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p><p class="paragraph">Default: <code class="lang-kotlin">25.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-score-drop-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-score-drop-factor.html
deleted file mode 100644
index 452c8955..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-score-drop-factor.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>rankingScoreDropFactor</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ranking-score-drop-factor.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/rankingScoreDropFactor/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">rankingScoreDropFactor</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>ranking</span><wbr></wbr><span>Score</span><wbr></wbr><span>Drop</span><wbr></wbr><span><span>Factor</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.95</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/raw.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/raw.html
deleted file mode 100644
index c4dcd3f4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/raw.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>raw</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/raw.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/raw/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">raw</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>raw</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-max.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-max.html
deleted file mode 100644
index fe086605..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-max.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>reassignMax</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-max.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/reassignMax/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">reassignMax</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>reassign</span><wbr></wbr><span><span>Max</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-overlap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-overlap.html
deleted file mode 100644
index 9a576ea0..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-overlap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>reassignOverlap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-overlap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/reassignOverlap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">reassignOverlap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>reassign</span><wbr></wbr><span><span>Overlap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.3</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-ratio.html
deleted file mode 100644
index 34357d78..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-ratio.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>reassignRatio</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reassign-ratio.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/reassignRatio/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">reassignRatio</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>reassign</span><wbr></wbr><span><span>Ratio</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/relaxed-e-value-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/relaxed-e-value-factor.html
deleted file mode 100644
index 1bad3566..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/relaxed-e-value-factor.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>relaxedEValueFactor</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/relaxed-e-value-factor.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/relaxedEValueFactor/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">relaxedEValueFactor</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>relaxed</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Factor</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/resume.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/resume.html
deleted file mode 100644
index fddebff5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/resume.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>resume</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/resume.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/resume/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">resume</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>resume</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--resume</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reverse.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reverse.html
deleted file mode 100644
index e94e3ffb..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reverse.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>reverse</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/reverse.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/reverse/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">reverse</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>reverse</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rho.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rho.html
deleted file mode 100644
index 7ea4c7b2..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rho.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>rho</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/rho.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/rho/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">rho</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>rho</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.99</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-estimate-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-estimate-factor.html
deleted file mode 100644
index 7238d72e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-estimate-factor.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>scoreEstimateFactor</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-estimate-factor.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/scoreEstimateFactor/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">scoreEstimateFactor</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>score</span><wbr></wbr><span>Estimate</span><wbr></wbr><span><span>Factor</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-ratio.html
deleted file mode 100644
index f90b0220..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-ratio.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>scoreRatio</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/score-ratio.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/scoreRatio/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">scoreRatio</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>score</span><wbr></wbr><span><span>Ratio</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.9</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-hit-density.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-hit-density.html
deleted file mode 100644
index b78bd7c4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-hit-density.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>seedHitDensity</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-hit-density.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/seedHitDensity/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">seedHitDensity</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>seed</span><wbr></wbr><span>Hit</span><wbr></wbr><span><span>Density</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-weight.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-weight.html
deleted file mode 100644
index e6a8cb3d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-weight.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>seedWeight</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/seed-weight.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/seedWeight/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">seedWeight</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>seed</span><wbr></wbr><span><span>Weight</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p><p class="paragraph">Default: <code class="lang-kotlin">7u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/self.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/self.html
deleted file mode 100644
index d6e22bf4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/self.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>self</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/self.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/self/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">self</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>self</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-max-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-max-len.html
deleted file mode 100644
index a853a712..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-max-len.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>shortQueryMaxLen</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-max-len.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/shortQueryMaxLen/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">shortQueryMaxLen</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>short</span><wbr></wbr><span>Query</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Len</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">60</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-ungapped-bit-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-ungapped-bit-score.html
deleted file mode 100644
index 53fbb6f7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-ungapped-bit-score.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>shortQueryUngappedBitScore</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-query-ungapped-bit-score.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/shortQueryUngappedBitScore/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">shortQueryUngappedBitScore</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>short</span><wbr></wbr><span>Query</span><wbr></wbr><span>Ungapped</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p><p class="paragraph">Default: <code class="lang-kotlin">25.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-seq-i-ds.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-seq-i-ds.html
deleted file mode 100644
index 38f113fc..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-seq-i-ds.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>shortSeqIDs</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/short-seq-i-ds.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/shortSeqIDs/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">shortSeqIDs</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>short</span><wbr></wbr><span>Seq</span><wbr></wbr><span><span>IDs</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/simple-freq.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/simple-freq.html
deleted file mode 100644
index e57e81fc..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/simple-freq.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>simpleFreq</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/simple-freq.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/simpleFreq/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">simpleFreq</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>simple</span><wbr></wbr><span><span>Freq</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sketch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sketch-size.html
deleted file mode 100644
index c4112986..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sketch-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>sketchSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sketch-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/sketchSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">sketchSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>sketch</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sort-join.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sort-join.html
deleted file mode 100644
index 21a5a9c4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sort-join.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>sortJoin</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/sort-join.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/sortJoin/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">sortJoin</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>sort</span><wbr></wbr><span><span>Join</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/space-penalty.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/space-penalty.html
deleted file mode 100644
index 45c9456a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/space-penalty.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>spacePenalty</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/space-penalty.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/spacePenalty/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">spacePenalty</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>space</span><wbr></wbr><span><span>Penalty</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/store-query-quality.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/store-query-quality.html
deleted file mode 100644
index c802dd5a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/store-query-quality.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>storeQueryQuality</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/store-query-quality.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/storeQueryQuality/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">storeQueryQuality</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>store</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Quality</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/strict-g-v-c.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/strict-g-v-c.html
deleted file mode 100644
index e31dd33e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/strict-g-v-c.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>strictGVC</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/strict-g-v-c.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/strictGVC/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">strictGVC</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>strict</span><wbr></wbr><span><span>GVC</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/superblock.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/superblock.html
deleted file mode 100644
index dcc3703c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/superblock.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>superblock</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/superblock.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/superblock/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">superblock</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>superblock</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p><p class="paragraph">Default: <code class="lang-kotlin">128</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-chunk-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-chunk-size.html
deleted file mode 100644
index 900da321..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-chunk-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>swipeChunkSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-chunk-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/swipeChunkSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">swipeChunkSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>swipe</span><wbr></wbr><span>Chunk</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">256u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-task-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-task-size.html
deleted file mode 100644
index f756db86..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-task-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>swipeTaskSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/swipe-task-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/swipeTaskSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">swipeTaskSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>swipe</span><wbr></wbr><span>Task</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">100000000</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-max-repeat-offset.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-max-repeat-offset.html
deleted file mode 100644
index bccd6218..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-max-repeat-offset.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>tantanMaxRepeatOffset</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-max-repeat-offset.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/tantanMaxRepeatOffset/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">tantanMaxRepeatOffset</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>tantan</span><wbr></wbr><span>Max</span><wbr></wbr><span>Repeat</span><wbr></wbr><span><span>Offset</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Maximum tandem repeat period to consider (50)</p><p class="paragraph">Flag: <code class="lang-kotlin">--tantan-maxRepeatOffset</code> // TODO: the caps are in the diamond cli source, are flag strings case sensitive?</p><p class="paragraph">Default: <code class="lang-kotlin">15</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-ungapped.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-ungapped.html
deleted file mode 100644
index 81dfac04..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-ungapped.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>tantanUngapped</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tantan-ungapped.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/tantanUngapped/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">tantanUngapped</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>tantan</span><wbr></wbr><span><span>Ungapped</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Use tantan masking in ungapped mode</p><p class="paragraph">Flag: <code class="lang-kotlin">--tantan-ungapped</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-bias.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-bias.html
deleted file mode 100644
index ea4b0e4e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-bias.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>targetBias</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-bias.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/targetBias/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">targetBias</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>target</span><wbr></wbr><span><span>Bias</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-fetch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-fetch-size.html
deleted file mode 100644
index 1bc5d6ce..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-fetch-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>targetFetchSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-fetch-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/targetFetchSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">targetFetchSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>target</span><wbr></wbr><span>Fetch</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Number of target sequences to fetch for seed extension.</p><p class="paragraph">Flag: <code class="lang-kotlin">--target-fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">4u</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-hard-cap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-hard-cap.html
deleted file mode 100644
index 3ac94f49..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-hard-cap.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>targetHardCap</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-hard-cap.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/targetHardCap/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">targetHardCap</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>target</span><wbr></wbr><span>Hard</span><wbr></wbr><span><span>Cap</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-parallel-verbosity.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-parallel-verbosity.html
deleted file mode 100644
index 1da60b06..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-parallel-verbosity.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>targetParallelVerbosity</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/target-parallel-verbosity.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/targetParallelVerbosity/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">targetParallelVerbosity</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>target</span><wbr></wbr><span>Parallel</span><wbr></wbr><span><span>Verbosity</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tile-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tile-size.html
deleted file mode 100644
index f6082e4f..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tile-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>tileSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tile-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/tileSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">tileSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>tile</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">1024</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/timeout.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/timeout.html
deleted file mode 100644
index 98748f24..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/timeout.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>timeout</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/timeout.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/timeout/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">timeout</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>timeout</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/trace-pt-fetch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/trace-pt-fetch-size.html
deleted file mode 100644
index e9db8d20..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/trace-pt-fetch-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>tracePtFetchSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/trace-pt-fetch-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/tracePtFetchSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">tracePtFetchSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>trace</span><wbr></wbr><span>Pt</span><wbr></wbr><span>Fetch</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">10e9</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/transcript-len-estimate.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/transcript-len-estimate.html
deleted file mode 100644
index fb2d6084..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/transcript-len-estimate.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>transcriptLenEstimate</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/transcript-len-estimate.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/transcriptLenEstimate/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">transcriptLenEstimate</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>transcript</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Estimate</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tree.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tree.html
deleted file mode 100644
index 26f6f3e3..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tree.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>tree</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tree.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/tree/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">tree</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>tree</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tsv-read-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tsv-read-size.html
deleted file mode 100644
index 824ee073..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tsv-read-size.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>tsvReadSize</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/tsv-read-size.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/tsvReadSize/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">tsvReadSize</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>tsv</span><wbr></wbr><span>Read</span><wbr></wbr><span><span>Size</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">1073741824</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/type.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/type.html
deleted file mode 100644
index 62556a33..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/type.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>type</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/type.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/type/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">type</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span><span>type</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="type.html">type</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-benchmark-type/index.html">BenchmarkType</a></div><p class="paragraph">TODO: seems to only be used by benchmark?</p><p class="paragraph">Flag: <code class="lang-kotlin">--type</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value-short.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value-short.html
deleted file mode 100644
index de3190e7..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value-short.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ungappedEValueShort</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value-short.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/ungappedEValueShort/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">ungappedEValueShort</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>ungapped</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Short</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value.html
deleted file mode 100644
index 082af672..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ungappedEValue</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-e-value.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/ungappedEValue/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">ungappedEValue</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>ungapped</span><wbr></wbr><span><span>EValue</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-window.html
deleted file mode 100644
index 34a389d2..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-window.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ungappedWindow</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/ungapped-window.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/ungappedWindow/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">ungappedWindow</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>ungapped</span><wbr></wbr><span><span>Window</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">48</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-dist.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-dist.html
deleted file mode 100644
index ea2f9cb5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-dist.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>upGmaDist</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-dist.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/upGmaDist/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">upGmaDist</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span><span>Dist</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-distribution-type/index.html">DistributionType</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-edge-limit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-edge-limit.html
deleted file mode 100644
index 208c289e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-edge-limit.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>upGmaEdgeLimit</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-edge-limit.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/upGmaEdgeLimit/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">upGmaEdgeLimit</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span>Edge</span><wbr></wbr><span><span>Limit</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p><p class="paragraph">Default: <code class="lang-kotlin">10000000</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-input.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-input.html
deleted file mode 100644
index 0bc38f9e..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-input.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>upGmaInput</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/up-gma-input.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/upGmaInput/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">upGmaInput</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span><span>Input</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts/-input-type/index.html">InputType</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-dataset-field.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-dataset-field.html
deleted file mode 100644
index 7deff911..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-dataset-field.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>useDatasetField</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-dataset-field.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/useDatasetField/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">useDatasetField</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>use</span><wbr></wbr><span>Dataset</span><wbr></wbr><span><span>Field</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-smith-waterman.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-smith-waterman.html
deleted file mode 100644
index 20cc2203..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-smith-waterman.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>useSmithWaterman</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/use-smith-waterman.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/useSmithWaterman/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">useSmithWaterman</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>use</span><wbr></wbr><span>Smith</span><wbr></wbr><span><span>Waterman</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/weighted-g-v-c.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/weighted-g-v-c.html
deleted file mode 100644
index b236cad8..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/weighted-g-v-c.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>weightedGVC</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/weighted-g-v-c.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/HiddenOptionContainerImpl/weightedGVC/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">HiddenOptionContainerImpl</a><span class="delimiter">/</span><span class="current">weightedGVC</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>weighted</span><wbr></wbr><span><span>GVC</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/-output-format-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/-output-format-option-container-impl.html
deleted file mode 100644
index 5a87bb1c..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/-output-format-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>OutputFormatOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/-output-format-option-container-impl.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/OutputFormatOptionContainerImpl/OutputFormatOptionContainerImpl/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">OutputFormatOptionContainerImpl</a><span class="delimiter">/</span><span class="current">OutputFormatOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Output</span><wbr></wbr><span>Format</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/include-lineage.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/include-lineage.html
deleted file mode 100644
index 194059d5..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/include-lineage.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>includeLineage</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/include-lineage.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/OutputFormatOptionContainerImpl/includeLineage/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">OutputFormatOptionContainerImpl</a><span class="delimiter">/</span><span class="current">includeLineage</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>include</span><wbr></wbr><span><span>Lineage</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="include-lineage.html">includeLineage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Include lineage in the taxonomic classification format.</p><p class="paragraph">Flag = <code class="lang-kotlin">--include-lineage</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/index.html
deleted file mode 100644
index 94ee54ac..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/index.html
+++ /dev/null
@@ -1,139 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>OutputFormatOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
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-        const savedDarkMode = JSON.parse(storage)
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-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/index.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="classlike" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/OutputFormatOptionContainerImpl///PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><span class="current">OutputFormatOptionContainerImpl</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>Output</span><wbr></wbr><span>Format</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="index.html">OutputFormatOptionContainerImpl</a> : <a href="../../org.veupathdb.lib.cli.diamond.opts/-output-format-option-container/index.html">OutputFormatOptionContainer</a></div></div></div>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="CONSTRUCTOR">
-        <h2 class="">Constructors</h2>
-        <div class="table"><a data-name="-1838344059%2FConstructors%2F769193423" anchor-label="OutputFormatOptionContainerImpl" id="-1838344059%2FConstructors%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-togglable="CONSTRUCTOR" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-output-format-option-container-impl.html"><span>Output</span><wbr></wbr><span>Format</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1838344059%2FConstructors%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">constructor</span><span class="token punctuation">(</span><span class="token punctuation">)</span></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-      <div data-togglable="PROPERTY">
-        <h2 class="">Properties</h2>
-        <div class="table"><a data-name="1423351902%2FProperties%2F769193423" anchor-label="includeLineage" id="1423351902%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="include-lineage.html"><span>include</span><wbr></wbr><span><span>Lineage</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1423351902%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="include-lineage.html">includeLineage</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Include lineage in the taxonomic classification format.</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-473275031%2FProperties%2F769193423" anchor-label="outputFormat" id="-473275031%2FProperties%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="output-format.html"><span>output</span><wbr></wbr><span><span>Format</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-473275031%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-format.html">outputFormat</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts.output_format/-output-format-options/index.html">OutputFormatOptions</a></div><div class="brief "><p class="paragraph">Flag = <code class="lang-kotlin">--outfmt</code> | <code class="lang-kotlin">-f</code></p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/output-format.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/output-format.html
deleted file mode 100644
index 98eb66a4..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/output-format.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>outputFormat</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
-        const osDarkSchemePreferred = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches
-        if (osDarkSchemePreferred === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    } else {
-        const savedDarkMode = JSON.parse(storage)
-        if(savedDarkMode === true) {
-            document.getElementsByTagName("html")[0].classList.add("theme-dark")
-        }
-    }
-    </script>
-<script type="text/javascript" src="https://unpkg.com/kotlin-playground@1/dist/playground.min.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/sourceset_dependencies.js" async="async"></script>
-<link href="../../../styles/style.css" rel="Stylesheet">
-<link href="../../../styles/main.css" rel="Stylesheet">
-<link href="../../../styles/prism.css" rel="Stylesheet">
-<link href="../../../styles/logo-styles.css" rel="Stylesheet">
-<link href="../../../styles/font-jb-sans-auto.css" rel="Stylesheet">
-<script type="text/javascript" src="../../../scripts/clipboard.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/navigation-loader.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/platform-content-handler.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/main.js" defer="defer"></script>
-<script type="text/javascript" src="../../../scripts/prism.js" async="async"></script>
-<script type="text/javascript" src="../../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../../index.html">
-                            diamondcli
-                    </a>
-            </div>
-            <div class="library-version">
-<dokka-template-command data="{&quot;@class&quot;:&quot;org.jetbrains.dokka.base.templating.ReplaceVersionsCommand&quot;,&quot;location&quot;:&quot;diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/output-format.html&quot;}">v0.1.0</dokka-template-command>            </div>
-        </div>
-        <div class="filter-section" id="filter-section">
-                <button class="platform-tag platform-selector jvm-like" data-active="" data-filter=":dokkaHtml/main">jvm</button>
-        </div>
-    </div>
-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="member" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl/OutputFormatOptionContainerImpl/outputFormat/#/PointingToDeclaration//769193423">
-  <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts.impl</a><span class="delimiter">/</span><a href="index.html">OutputFormatOptionContainerImpl</a><span class="delimiter">/</span><span class="current">outputFormat</span></div>
-  <div class="cover ">
-    <h1 class="cover"><span>output</span><wbr></wbr><span><span>Format</span></span></h1>
-  </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="output-format.html">outputFormat</a><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.opts.output_format/-output-format-options/index.html">OutputFormatOptions</a></div><p class="paragraph">Flag = <code class="lang-kotlin">--outfmt</code> | <code class="lang-kotlin">-f</code></p></div></div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/-view-align-option-container-impl.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/-view-align-option-container-impl.html
deleted file mode 100644
index 7306d26a..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/-view-align-option-container-impl.html
+++ /dev/null
@@ -1,81 +0,0 @@
-<!DOCTYPE html>
-<html class="no-js">
-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>ViewAlignOptionContainerImpl</title>
-    <link href="../../../images/logo-icon.svg" rel="icon" type="image/svg">
-    <script>var pathToRoot = "../../../";</script>
-    <script>document.documentElement.classList.replace("no-js","js");</script>
-    <script>const storage = localStorage.getItem("dokka-dark-mode")
-    if (storage == null) {
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/daa.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/daa.html
deleted file mode 100644
index 4276844d..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/daa.html
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-            <div class="library-name">
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-                            diamondcli
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-            </div>
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-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/index.html
deleted file mode 100644
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--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/index.html
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-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
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-                            diamondcli
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-    <h1 class="cover"><span>View</span><wbr></wbr><span>Align</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></h1>
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-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-844235109%2FProperties%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">open </span><span class="token keyword">override </span><span class="token keyword">var </span><a href="daa.html">daa</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">DIAMOND alignment archive (DAA) file</p></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/index.html
deleted file mode 100644
index 740a60fc..00000000
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/index.html
+++ /dev/null
@@ -1,344 +0,0 @@
-<!DOCTYPE html>
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-<head>
-    <meta name="viewport" content="width=device-width, initial-scale=1" charset="UTF-8">
-    <title>org.veupathdb.lib.cli.diamond.opts.impl</title>
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-    <script>var pathToRoot = "../../";</script>
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-<link href="../../styles/style.css" rel="Stylesheet">
-<link href="../../styles/main.css" rel="Stylesheet">
-<link href="../../styles/prism.css" rel="Stylesheet">
-<link href="../../styles/logo-styles.css" rel="Stylesheet">
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-<script type="text/javascript" src="../../scripts/symbol-parameters-wrapper_deferred.js" defer="defer"></script>
-<link href="../../styles/multimodule.css" rel="Stylesheet">
-</head>
-<body>
-    <div class="root">
-<nav class="navigation" id="navigation-wrapper">
-    <div class="navigation--inner">
-        <div class="navigation-title">
-            <button class="menu-toggle" id="menu-toggle" type="button">toggle menu</button>
-            <div class="library-name">
-                    <a class="library-name--link" href="../../index.html">
-                            diamondcli
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-            </div>
-            <div class="library-version">
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-    <div class="navigation-controls">
-        <button class="navigation-controls--btn navigation-controls--theme" id="theme-toggle-button" type="button">switch theme</button>
-        <div class="navigation-controls--btn navigation-controls--search" id="searchBar" role="button">search in API</div>
-    </div>
-</nav>
-        <div id="container">
-            <div class="sidebar" id="leftColumn">
-                <div class="sidebar--inner" id="sideMenu"></div>
-            </div>
-            <div id="main">
-<div class="main-content" data-page-type="package" id="content" pageIds="diamondcli::org.veupathdb.lib.cli.diamond.opts.impl////PointingToDeclaration//769193423">
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-  <div class="cover ">
-    <h1 class="cover"><span><span>Package-level</span></span> <span><span>declarations</span></span></h1>
-  </div>
-  <div class="tabbedcontent">
-    <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="TYPE">Types</button></div>
-    <div class="tabs-section-body">
-      <div data-togglable="TYPE">
-        <h2 class="">Types</h2>
-        <div class="table"><a data-name="-165811030%2FClasslikes%2F769193423" anchor-label="AdvancedGeneralOptionContainerImpl" id="-165811030%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-advanced-general-option-container-impl/index.html"><span>Advanced</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-165811030%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-advanced-general-option-container-impl/index.html">AdvancedGeneralOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html">AdvancedGeneralOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-806193206%2FClasslikes%2F769193423" anchor-label="AdvancedQueryOptionContainerImpl" id="-806193206%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-advanced-query-option-container-impl/index.html"><span>Advanced</span><wbr></wbr><span>Query</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-806193206%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-advanced-query-option-container-impl/index.html">AdvancedQueryOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html">AdvancedQueryOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="760525886%2FClasslikes%2F769193423" anchor-label="AlignerClusteringOptionContainerImpl" id="760525886%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-clustering-option-container-impl/index.html"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="760525886%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-aligner-clustering-option-container-impl/index.html">AlignerClusteringOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-option-container/index.html">AlignerClusteringOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="626376510%2FClasslikes%2F769193423" anchor-label="AlignerClusteringRealignOptionContainerImpl" id="626376510%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-clustering-realign-option-container-impl/index.html"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Realign</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="626376510%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-aligner-clustering-realign-option-container-impl/index.html">AlignerClusteringRealignOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-realign-option-container/index.html">AlignerClusteringRealignOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1710684668%2FClasslikes%2F769193423" anchor-label="AlignerGeneralOptionContainerImpl" id="1710684668%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-general-option-container-impl/index.html"><span>Aligner</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1710684668%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-aligner-general-option-container-impl/index.html">AlignerGeneralOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-aligner-general-option-container/index.html">AlignerGeneralOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2009695821%2FClasslikes%2F769193423" anchor-label="AlignerSensitivityOptionContainerImpl" id="-2009695821%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-sensitivity-option-container-impl/index.html"><span>Aligner</span><wbr></wbr><span>Sensitivity</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2009695821%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-aligner-sensitivity-option-container-impl/index.html">AlignerSensitivityOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-aligner-sensitivity-option-container/index.html">AlignerSensitivityOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="720084091%2FClasslikes%2F769193423" anchor-label="AlignerViewOptionContainerImpl" id="720084091%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-aligner-view-option-container-impl/index.html"><span>Aligner</span><wbr></wbr><span>View</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="720084091%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-aligner-view-option-container-impl/index.html">AlignerViewOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-aligner-view-option-container/index.html">AlignerViewOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1662772132%2FClasslikes%2F769193423" anchor-label="ClusteringGeneralOptionContainerImpl" id="1662772132%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-clustering-general-option-container-impl/index.html"><span>Clustering</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1662772132%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-clustering-general-option-container-impl/index.html">ClusteringGeneralOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-clustering-general-option-container/index.html">ClusteringGeneralOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1522608454%2FClasslikes%2F769193423" anchor-label="ClusteringInputOptionContainerImpl" id="1522608454%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-clustering-input-option-container-impl/index.html"><span>Clustering</span><wbr></wbr><span>Input</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1522608454%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-clustering-input-option-container-impl/index.html">ClusteringInputOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-clustering-input-option-container/index.html">ClusteringInputOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="31904272%2FClasslikes%2F769193423" anchor-label="ClusteringReassignOptionContainerImpl" id="31904272%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-clustering-reassign-option-container-impl/index.html"><span>Clustering</span><wbr></wbr><span>Reassign</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="31904272%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-clustering-reassign-option-container-impl/index.html">ClusteringReassignOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-clustering-reassign-option-container/index.html">ClusteringReassignOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-239742742%2FClasslikes%2F769193423" anchor-label="GeneralDBOptionContainerImpl" id="-239742742%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-d-b-option-container-impl/index.html"><span>General</span><wbr></wbr><span>DBOption</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-239742742%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-general-d-b-option-container-impl/index.html">GeneralDBOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-general-d-b-option-container/index.html">GeneralDBOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-2113651924%2FClasslikes%2F769193423" anchor-label="GeneralOptionContainerImpl" id="-2113651924%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-option-container-impl/index.html"><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-2113651924%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-general-option-container-impl/index.html">GeneralOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-general-option-container/index.html">GeneralOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1324585658%2FClasslikes%2F769193423" anchor-label="GeneralOutputHeaderOptionContainerImpl" id="1324585658%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-output-header-option-container-impl/index.html"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Header</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1324585658%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-general-output-header-option-container-impl/index.html">GeneralOutputHeaderOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-general-output-header-option-container/index.html">GeneralOutputHeaderOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1734698611%2FClasslikes%2F769193423" anchor-label="GeneralOutputOptionContainerImpl" id="-1734698611%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-general-output-option-container-impl/index.html"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1734698611%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-general-output-option-container-impl/index.html">GeneralOutputOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-general-output-option-container/index.html">GeneralOutputOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="1793070224%2FClasslikes%2F769193423" anchor-label="HiddenOptionContainerImpl" id="1793070224%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-hidden-option-container-impl/index.html"><span>Hidden</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="1793070224%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-hidden-option-container-impl/index.html">HiddenOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html">HiddenOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-511150722%2FClasslikes%2F769193423" anchor-label="OutputFormatOptionContainerImpl" id="-511150722%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-output-format-option-container-impl/index.html"><span>Output</span><wbr></wbr><span>Format</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-511150722%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-output-format-option-container-impl/index.html">OutputFormatOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-output-format-option-container/index.html">OutputFormatOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-<a data-name="-1367599644%2FClasslikes%2F769193423" anchor-label="ViewAlignOptionContainerImpl" id="-1367599644%2FClasslikes%2F769193423" data-filterable-set=":dokkaHtml/main"></a>
-          <div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main">
-            <div class="main-subrow keyValue ">
-              <div class=""><span class="inline-flex">
-                  <div><a href="-view-align-option-container-impl/index.html"><span>View</span><wbr></wbr><span>Align</span><wbr></wbr><span>Option</span><wbr></wbr><span>Container</span><wbr></wbr><span><span>Impl</span></span></a></div>
-<span class="anchor-wrapper"><span class="anchor-icon" pointing-to="-1367599644%2FClasslikes%2F769193423"></span>
-                    <div class="copy-popup-wrapper "><span class="copy-popup-icon"></span><span>Link copied to clipboard</span></div>
-                  </span></span></div>
-              <div>
-                <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">class </span><a href="-view-align-option-container-impl/index.html">ViewAlignOptionContainerImpl</a> : <a href="../org.veupathdb.lib.cli.diamond.opts/-view-align-option-container/index.html">ViewAlignOptionContainer</a></div></div></div>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-      <div class="footer">
-        <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
-                class="pull-right"><span>Generated by </span><a
-                href="https://github.com/Kotlin/dokka"><span>dokka</span><span class="padded-icon"></span></a></span>
-      </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html
index 59df7b9a..ffd5df22 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-general-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">AdvancedGeneralOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Advanced</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AdvancedGeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/index.html">AdvancedGeneralOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AdvancedGeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html
index a7ed789a..f25dde14 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-advanced-query-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">AdvancedQueryOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Advanced</span><wbr></wbr><span>Query</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AdvancedQueryOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/index.html">AdvancedQueryOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AdvancedQueryOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-option-container/index.html
index 030481b7..093c996d 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">AlignerClusteringOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerClusteringOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-option-container-impl/index.html">AlignerClusteringOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerClusteringOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-realign-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-realign-option-container/index.html
index 434478dd..76321680 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-realign-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-clustering-realign-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">AlignerClusteringRealignOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Clustering</span><wbr></wbr><span>Realign</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerClusteringRealignOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-aligner-clustering-realign-option-container-impl/index.html">AlignerClusteringRealignOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerClusteringRealignOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-general-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-general-option-container/index.html
index b3259bdd..026d1371 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-general-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-general-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">AlignerGeneralOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Aligner</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerGeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-aligner-general-option-container-impl/index.html">AlignerGeneralOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerGeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-sensitivity-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-sensitivity-option-container/index.html
index 84f05150..59cda735 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-sensitivity-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-sensitivity-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">AlignerSensitivityOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Aligner</span><wbr></wbr><span>Sensitivity</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerSensitivityOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-aligner-sensitivity-option-container-impl/index.html">AlignerSensitivityOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerSensitivityOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-view-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-view-option-container/index.html
index 2f0f55d6..84a722d9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-view-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-aligner-view-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">AlignerViewOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Aligner</span><wbr></wbr><span>View</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerViewOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-aligner-view-option-container-impl/index.html">AlignerViewOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">AlignerViewOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-general-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-general-option-container/index.html
index 18375322..e0041ea7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-general-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-general-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">ClusteringGeneralOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Clustering</span><wbr></wbr><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">ClusteringGeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-clustering-general-option-container-impl/index.html">ClusteringGeneralOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">ClusteringGeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-input-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-input-option-container/index.html
index db1cec94..5e198207 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-input-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-input-option-container/index.html
@@ -66,7 +66,7 @@
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-reassign-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-clustering-reassign-option-container/index.html
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/-comp-based-stats-and-matrix-adjust/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/-comp-based-stats-and-matrix-adjust/index.html
index d2a6bc1e..50c7816c 100644
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/-comp-based-stats/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/-comp-based-stats/index.html
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/-hauser-global/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/-hauser-global/index.html
index 4b9cf448..f5120a3f 100644
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diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-composition-based-stats/index.html
index aa26b434..6d902550 100644
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data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html">DBInfo</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html">PrepDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-general-d-b-option-container-impl/index.html">GeneralDBOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">GeneralDBOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html">DBInfo</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html">PrepDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-option-container/index.html
index cc943996..6f6bc876 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">GeneralOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>General</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">GeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html">DBInfo</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html">MergeDAA</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html">PrepDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-general-option-container-impl/index.html">GeneralOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">GeneralOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html">DBInfo</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html">MergeDAA</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html">PrepDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-header-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-header-option-container/index.html
index e128fb65..e43896d2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-header-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-header-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">GeneralOutputHeaderOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Header</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">GeneralOutputHeaderOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-general-output-header-option-container-impl/index.html">GeneralOutputHeaderOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">GeneralOutputHeaderOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-option-container/index.html
index c7614cd1..c483fd2f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-general-output-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">GeneralOutputOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>General</span><wbr></wbr><span>Output</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">GeneralOutputOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html">MergeDAA</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-general-output-option-container-impl/index.html">GeneralOutputOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">GeneralOutputOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html">MergeDAA</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html
index d262ce22..bb1dcc34 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/add-self-aln.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>add</span><wbr></wbr><span>Self</span><wbr></wbr><span><span>Aln</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html
index d2bdefc4..2f171383 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/aln-out.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>aln</span><wbr></wbr><span><span>Out</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html
index 8f543162..6ff8b448 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-score.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>anchor</span><wbr></wbr><span><span>Score</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html
index 48334229..f8e54889 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchor-window.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>anchor</span><wbr></wbr><span><span>Window</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">12</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">12</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html
index af7215c3..71f41f99 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/anchored-swipe.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>anchored</span><wbr></wbr><span><span>Swipe</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html
index 94545066..1833867f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ants.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>ants</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p><p class="paragraph">Default: <code class="lang-kotlin">100</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p><p class="paragraph">Default: <code class="lang-kotlin">100</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html
index 6336f613..a5c5e399 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/approx-backtrace.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>approx</span><wbr></wbr><span><span>Backtrace</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html
index 0a8ac694..18108387 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-cutoff.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>b</span><wbr></wbr><span><span>Cutoff</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html
index 37398f4f..4ccc8cbe 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-match.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>b</span><wbr></wbr><span><span>Match</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html
index 953283aa..87ebbf7f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/b-mismatch.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>b</span><wbr></wbr><span><span>Mismatch</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html
index 89429593..f06b9ff9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/band-bin.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>band</span><wbr></wbr><span><span>Bin</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p><p class="paragraph">Default: <code class="lang-kotlin">24</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p><p class="paragraph">Default: <code class="lang-kotlin">24</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html
index d69d71fa..35c12195 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/bootstrap-block.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>bootstrap</span><wbr></wbr><span><span>Block</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p><p class="paragraph">Default: <code class="lang-kotlin">1000000</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p><p class="paragraph">Default: <code class="lang-kotlin">1000000</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html
index d260c5eb..9f32f509 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-angle.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cbs</span><wbr></wbr><span><span>Angle</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html
index 7d2a2c0c..1ba1e40d 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-err-tolerance.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cbs</span><wbr></wbr><span>Err</span><wbr></wbr><span><span>Tolerance</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.00000001</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.00000001</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html
index 2c453880..2f1fd2c4 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-it-limit.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cbs</span><wbr></wbr><span>It</span><wbr></wbr><span><span>Limit</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html
index e4d2f65f..e3395ffd 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-matrix-scale.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cbs</span><wbr></wbr><span>Matrix</span><wbr></wbr><span><span>Scale</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p><p class="paragraph">Default: <code class="lang-kotlin">1</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p><p class="paragraph">Default: <code class="lang-kotlin">1</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html
index 68cf4fbd..4854ed92 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cbs-window.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cbs</span><wbr></wbr><span><span>Window</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">40</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">40</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html
index d9053157..b02444fa 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/centroid-factor.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>centroid</span><wbr></wbr><span><span>Factor</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">3</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">3</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html
index a902a9ca..a17fe102 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-len-cap.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>chaining</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Cap</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p><p class="paragraph">Default: <code class="lang-kotlin">2.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p><p class="paragraph">Default: <code class="lang-kotlin">2.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html
index 5eaf58e9..e373eb97 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-gap.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>chaining</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Gap</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html
index f7cc4af1..7829aed2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-max-nodes.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>chaining</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Nodes</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html
index 6b98eca2..a6bdaca9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-min-nodes.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>chaining</span><wbr></wbr><span>Min</span><wbr></wbr><span><span>Nodes</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p><p class="paragraph">Default: <code class="lang-kotlin">200</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p><p class="paragraph">Default: <code class="lang-kotlin">200</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html
index 3cdd3222..b38c1d04 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-range-cover.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>chaining</span><wbr></wbr><span>Range</span><wbr></wbr><span><span>Cover</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p><p class="paragraph">Default = <code class="lang-kotlin">8</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p><p class="paragraph">Default = <code class="lang-kotlin">8</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html
index 6d602acf..fedbc2f2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chaining-stacked-h-s-p-ratio.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>chaining</span><wbr></wbr><span>Stacked</span><wbr></wbr><span><span>HSPRatio</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html
index 6d72f483..e6625d37 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/chunk-size-multiplier.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>chunk</span><wbr></wbr><span>Size</span><wbr></wbr><span><span>Multiplier</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p><p class="paragraph">Default: <code class="lang-kotlin">4</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p><p class="paragraph">Default: <code class="lang-kotlin">4</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html
index 889de036..285fcf6b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/classic-band.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>classic</span><wbr></wbr><span><span>Band</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html
index aa899827..5ffe7379 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-algo.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Algo</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Clustering algorithm ('mcl')</p><p class="paragraph">TODO: actual values for this enum are dependent on compile flags, it seems     that &quot;cascaded&quot; is the only 'safe' option, &quot;mcl&quot; is dependent on a     compile flag.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-algo</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Clustering algorithm ('mcl')</p><p class="paragraph">TODO: actual values for this enum are dependent on compile flags, it seems     that &quot;cascaded&quot; is the only 'safe' option, &quot;mcl&quot; is dependent on a     compile flag.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-algo</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html
index 2efdc6f8..a82d0157 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-graph-file.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cluster</span><wbr></wbr><span>Graph</span><wbr></wbr><span><span>File</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-graph-file</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-graph-file</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html
index ba56ca0b..ef033a14 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-restart.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Restart</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Restart clustering from dumped graph.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-restart</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Restart clustering from dumped graph.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-restart</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html
index c75029c9..8ef87c0c 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-similarity.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Similarity</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Clustering similarity measure.</p><p class="paragraph">TODO: this is some sort of expression string, it's currently unclear what     its rules are.  This should be converted to a complex type for     validation.</p><p class="paragraph">TODO: only seems relevant to <code class="lang-kotlin">cluster</code>, <code class="lang-kotlin">deepclust</code>, <code class="lang-kotlin">linclust</code></p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-similarity</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">Clustering similarity measure.</p><p class="paragraph">TODO: this is some sort of expression string, it's currently unclear what     its rules are.  This should be converted to a complex type for     validation.</p><p class="paragraph">TODO: only seems relevant to <code class="lang-kotlin">cluster</code>, <code class="lang-kotlin">deepclust</code>, <code class="lang-kotlin">linclust</code></p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-similarity</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html
index 539de626..68b4c6a0 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cluster-threshold.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cluster</span><wbr></wbr><span><span>Threshold</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Threshold for the similarity measure.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Threshold for the similarity measure.</p><p class="paragraph">Flag: <code class="lang-kotlin">--cluster-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html
index 33f1e24b..81349477 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/col-bin.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>col</span><wbr></wbr><span><span>Bin</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p><p class="paragraph">Default: <code class="lang-kotlin">400</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p><p class="paragraph">Default: <code class="lang-kotlin">400</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html
index d354b4b2..460d42ee 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/cutoff-score8-bit.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>cutoff</span><wbr></wbr><span><span>Score8Bit</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p><p class="paragraph">Default: <code class="lang-kotlin">240</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p><p class="paragraph">Default: <code class="lang-kotlin">240</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html
index cf3a5232..2ea374e7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-exp.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>d</span><wbr></wbr><span><span>Exp</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html
index 1c7d3f1d..19c59605 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/d-new.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>d</span><wbr></wbr><span><span>New</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html
index a40da85f..c6381364 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/db-type.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>db</span><wbr></wbr><span><span>Type</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="db-type.html">dbType</a><span class="token operator">: </span><a href="../-sequence-type/index.html">SequenceType</a></div><p class="paragraph">Type of sequences in database file (nucl/prot).</p><p class="paragraph">Flag: <code class="lang-kotlin">--dbtype</code></p><p class="paragraph">Default: <a href="../-sequence-type/-amino-acid/index.html">SequenceType.AminoAcid</a></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="db-type.html">dbType</a><span class="token operator">: </span><a href="../-sequence-type/index.html">SequenceType</a></div><p class="paragraph">Type of sequences in database file (nucl/prot).</p><p class="paragraph">Flag: <code class="lang-kotlin">--dbtype</code></p><p class="paragraph">Default: <a href="../-sequence-type/-amino-acid/index.html">SequenceType.AminoAcid</a></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html
index f03a64af..f37577cd 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/deque-bucket-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>deque</span><wbr></wbr><span>Bucket</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p><p class="paragraph">Default: <code class="lang-kotlin">524288</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p><p class="paragraph">Default: <code class="lang-kotlin">524288</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html
index 8443185a..dac14109 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-cov.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>diag</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>Cov</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html
index c898720e..3a4a920e 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-filter-i-d.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>diag</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>ID</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html
index 30ac4bfa..85afbd65 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/diag-min-estimate.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>diag</span><wbr></wbr><span>Min</span><wbr></wbr><span><span>Estimate</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p><p class="paragraph">Default: <code class="lang-kotlin">17</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p><p class="paragraph">Default: <code class="lang-kotlin">17</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html
index 23a9b52a..8901ce56 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ext-yield.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>ext</span><wbr></wbr><span><span>Yield</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html
index 42ca521d..4ffa96ac 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-cap.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>family</span><wbr></wbr><span><span>Cap</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html
index 07dfeb01..c7f6ada9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/family-counts-file.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>family</span><wbr></wbr><span>Counts</span><wbr></wbr><span><span>File</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html
index 1c7c0899..1cb608fa 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fast-tsv.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>fast</span><wbr></wbr><span><span>Tsv</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html
index b44f840f..79438ca2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/fetch-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>fetch</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Trace point fetch size.</p><p class="paragraph">Flag: <code class="lang-kotlin">--fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">4096u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Trace point fetch size.</p><p class="paragraph">Flag: <code class="lang-kotlin">--fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">4096u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html
index f5c4ce0c..9819026a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file1.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>file1</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html
index 486c4707..673fd9f7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/file2.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>file2</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html
index 9ecde4c5..f610c0dd 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/freq-threshold.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>freq</span><wbr></wbr><span><span>Threshold</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html
index cb1e4740..ad816788 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/full-sw-len.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>full</span><wbr></wbr><span>Sw</span><wbr></wbr><span><span>Len</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html
index 79f2f9d3..3c9be8f3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-diag-bit-score.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span>Diag</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p><p class="paragraph">Default: <code class="lang-kotlin">12.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p><p class="paragraph">Default: <code class="lang-kotlin">12.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html
index affa484d..7328dcf3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-e-value1.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>EValue1</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p><p class="paragraph">Default: <code class="lang-kotlin">2000.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html
index ce2d74a1..7a35cb1f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/gapped-filter-window.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>gapped</span><wbr></wbr><span>Filter</span><wbr></wbr><span><span>Window</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">200</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">200</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html
index d2070e35..e4efc8dd 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/graph-algo.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>graph</span><wbr></wbr><span><span>Algo</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../-graph-algorithm/index.html">GraphAlgorithm</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p><p class="paragraph">Default: <a href="../-graph-algorithm/-greedy-vortex-cover/index.html">GraphAlgorithm.GreedyVortexCover</a></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../-graph-algorithm/index.html">GraphAlgorithm</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p><p class="paragraph">Default: <a href="../-graph-algorithm/-greedy-vortex-cover/index.html">GraphAlgorithm.GreedyVortexCover</a></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html
index da4cf66b..5f41d28f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hamming-ext.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>hamming</span><wbr></wbr><span><span>Ext</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html
index 19411e09..f6b724c2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hard-masked.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>hard</span><wbr></wbr><span><span>Masked</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html
index 2c66aab2..71cd483f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/hash-join-swap.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>hash</span><wbr></wbr><span>Join</span><wbr></wbr><span><span>Swap</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html
index 232e12dc..834c0ddf 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-left.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>id</span><wbr></wbr><span><span>Left</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html
index 346c8f87..1ed6b895 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-n.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>id</span><wbr></wbr><span><span>N</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html
index 91fe61bd..e8ec371e 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/id-right.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>id</span><wbr></wbr><span><span>Right</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html
index b752b279..23fe735d 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">HiddenOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Hidden</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">HiddenOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html">DBInfo</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html">MergeDAA</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html">PrepDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-hidden-option-container-impl/index.html">HiddenOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">HiddenOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster/index.html">Cluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-d-b-info/index.html">DBInfo</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-deep-clustering/index.html">DeepClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-get-seq/index.html">GetSeq</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-greedy-vortex-cover/index.html">GreedyVortexCover</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-linear-cluster/index.html">LinearCluster</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-d-b/index.html">MakeDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-make-index/index.html">MakeIndex</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-merge-d-a-a/index.html">MergeDAA</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-prep-d-b/index.html">PrepDB</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-reassign-clusters/index.html">ReassignClusters</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-recompute-clustering/index.html">RecomputeClustering</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
@@ -83,7 +83,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="add-self-aln.html">addSelfAln</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--add-self-aln</code></p></div></div></div>
                 </div>
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             </div>
@@ -98,7 +98,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="aln-out.html">alnOut</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--aln-out</code></p></div></div></div>
                 </div>
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@@ -113,7 +113,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchored-swipe.html">anchoredSwipe</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchored-swipe</code></p></div></div></div>
                 </div>
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@@ -128,7 +128,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-score.html">anchorScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -143,7 +143,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="anchor-window.html">anchorWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--anchor-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -158,7 +158,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ants.html">ants</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ants</code></p></div></div></div>
                 </div>
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@@ -173,7 +173,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="approx-backtrace.html">approxBacktrace</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--approx-backtrace</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -188,7 +188,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="band-bin.html">bandBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--band-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -203,7 +203,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-cutoff.html">bCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bcutoff</code></p></div></div></div>
                 </div>
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             </div>
@@ -218,7 +218,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-match.html">bMatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmatch</code></p></div></div></div>
                 </div>
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@@ -233,7 +233,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="b-mismatch.html">bMismatch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bmismatch</code></p></div></div></div>
                 </div>
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             </div>
@@ -248,7 +248,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="bootstrap-block.html">bootstrapBlock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--bootstrap-block</code></p></div></div></div>
                 </div>
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             </div>
@@ -263,7 +263,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-angle.html">cbsAngle</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-angle</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -278,7 +278,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-err-tolerance.html">cbsErrTolerance</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-err-tolerance</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -293,7 +293,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-it-limit.html">cbsItLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-it-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -308,7 +308,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-matrix-scale.html">cbsMatrixScale</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-matrix-scale</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -323,7 +323,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cbs-window.html">cbsWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cbs-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -338,7 +338,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="centroid-factor.html">centroidFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--centroid-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -353,7 +353,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-len-cap.html">chainingLenCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-len-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -368,7 +368,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-gap.html">chainingMaxGap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxgap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -383,7 +383,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-max-nodes.html">chainingMaxNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-maxnodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -398,7 +398,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-min-nodes.html">chainingMinNodes</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-min-nodes</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-range-cover.html">chainingRangeCover</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-range-cover</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chaining-stacked-h-s-p-ratio.html">chainingStackedHSPRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chaining-stacked-hsp-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="chunk-size-multiplier.html">chunkSizeMultiplier</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--chunk-size-multiplier</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="classic-band.html">classicBand</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--classic-band</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-algo.html">clusterAlgo</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering algorithm ('mcl')</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-graph-file.html">clusterGraphFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Filename for dumping the graph or reading the graph if cluster-restart.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-restart.html">clusterRestart</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Restart clustering from dumped graph.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-similarity.html">clusterSimilarity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">Clustering similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cluster-threshold.html">clusterThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Threshold for the similarity measure.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="col-bin.html">colBin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--col-bin</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="cutoff-score8-bit.html">cutoffScore8Bit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--cutoff-score-8bit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="db-type.html">dbType</a><span class="token operator">: </span><a href="../-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="db-type.html">dbType</a><span class="token operator">: </span><a href="../-sequence-type/index.html">SequenceType</a></div><div class="brief "><p class="paragraph">Type of sequences in database file (nucl/prot).</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="deque-bucket-size.html">dequeBucketSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--deque_bucket_size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-exp.html">dExp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_exp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-cov.html">diagFilterCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-cov</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-filter-i-d.html">diagFilterID</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-filter-id</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="diag-min-estimate.html">diagMinEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--diag-min-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="d-new.html">dNew</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--d_new</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ext-yield.html">extYield</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ext-yield</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-cap.html">familyCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="family-counts-file.html">familyCountsFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--family-counts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fast-tsv.html">fastTsv</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--fast-tsv</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="fetch-size.html">fetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Trace point fetch size.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file1.html">file1</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="file2.html">file2</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--file2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="freq-threshold.html">freqThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--freq-treshold</code> // TYPO: This typo exists in the diamond cli source.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="full-sw-len.html">fullSwLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--full-sw-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-diag-bit-score.html">gappedFilterDiagBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-diag-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-e-value1.html">gappedFilterEValue1</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-evalue1</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="gapped-filter-window.html">gappedFilterWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--gapped-filter-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -863,7 +863,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="graph-algo.html">graphAlgo</a><span class="token operator">: </span><a href="../-graph-algorithm/index.html">GraphAlgorithm</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--graph-algo</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -878,7 +878,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hamming-ext.html">hammingExt</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hamming-ext</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -893,7 +893,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hard-masked.html">hardMasked</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hard-masked</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -908,7 +908,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="hash-join-swap.html">hashJoinSwap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--hash_join_swap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -923,7 +923,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-left.html">idLeft</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idl</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -938,7 +938,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-n.html">idN</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idn</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -953,7 +953,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="id-right.html">idRight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--idr</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -968,7 +968,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -983,7 +983,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -998,7 +998,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1013,7 +1013,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1028,7 +1028,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1043,7 +1043,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1058,7 +1058,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1073,7 +1073,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1088,7 +1088,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1103,7 +1103,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1118,7 +1118,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1133,7 +1133,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1148,7 +1148,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Maximum seed frequency.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1163,7 +1163,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1178,7 +1178,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1193,7 +1193,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1208,7 +1208,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL chunk size per thread.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1223,7 +1223,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL expansion coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1238,7 +1238,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL inflation coefficient.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1253,7 +1253,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">MCL maximum iterations.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1268,7 +1268,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1283,7 +1283,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">MCL switch to sparse matrix computation.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1298,7 +1298,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Some stats about the connected components in MCL.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1313,7 +1313,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1328,7 +1328,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1343,7 +1343,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1358,7 +1358,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1373,7 +1373,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1388,7 +1388,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1403,7 +1403,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1418,7 +1418,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div></div>
                 </div>
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             </div>
@@ -1433,7 +1433,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1448,7 +1448,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1463,7 +1463,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1478,7 +1478,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1493,7 +1493,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1508,7 +1508,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1523,7 +1523,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1538,7 +1538,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1553,7 +1553,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1568,7 +1568,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1583,7 +1583,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1598,7 +1598,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1613,7 +1613,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1628,7 +1628,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1643,7 +1643,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1658,7 +1658,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1673,7 +1673,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1688,7 +1688,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1703,7 +1703,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1718,7 +1718,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1733,7 +1733,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1748,7 +1748,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1763,7 +1763,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1778,7 +1778,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1793,7 +1793,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1808,7 +1808,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1823,7 +1823,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1838,7 +1838,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1853,7 +1853,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1868,7 +1868,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1883,7 +1883,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1898,7 +1898,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1913,7 +1913,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1928,7 +1928,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><div class="brief "><p class="paragraph">TODO: this flag appears to be unused.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1943,7 +1943,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1958,7 +1958,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1973,7 +1973,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -1988,7 +1988,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2003,7 +2003,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2018,7 +2018,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2033,7 +2033,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2048,7 +2048,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2063,7 +2063,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2078,7 +2078,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2093,7 +2093,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2108,7 +2108,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2123,7 +2123,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2138,7 +2138,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2153,7 +2153,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2168,7 +2168,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2183,7 +2183,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2198,7 +2198,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2213,7 +2213,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2228,7 +2228,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Maximum tandem repeat period to consider (50)</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2243,7 +2243,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Use tantan masking in ungapped mode</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2258,7 +2258,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2273,7 +2273,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Number of target sequences to fetch for seed extension.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2288,7 +2288,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2303,7 +2303,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2318,7 +2318,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2333,7 +2333,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2348,7 +2348,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2363,7 +2363,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2378,7 +2378,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2393,7 +2393,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2408,7 +2408,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="type.html">type</a><span class="token operator">: </span><a href="../-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="type.html">type</a><span class="token operator">: </span><a href="../-benchmark-type/index.html">BenchmarkType</a></div><div class="brief "><p class="paragraph">TODO: seems to only be used by benchmark?</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2423,7 +2423,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2438,7 +2438,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2453,7 +2453,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2468,7 +2468,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../-distribution-type/index.html">DistributionType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2483,7 +2483,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2498,7 +2498,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../-input-type/index.html">InputType</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2513,7 +2513,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2528,7 +2528,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div></div>
                 </div>
               </div>
             </div>
@@ -2543,7 +2543,7 @@ <h2 class="">Properties</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><div class="brief "><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html
index e9df7206..b5b7f935 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-h-t-factor.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>join</span><wbr></wbr><span><span>HTFactor</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.3</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-h-t-factor.html">joinHTFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-ht-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.3</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html
index b3b8aa30..431b278c 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-key-len.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>join</span><wbr></wbr><span>Split</span><wbr></wbr><span>Key</span><wbr></wbr><span><span>Len</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">17u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-key-len.html">joinSplitKeyLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-key-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">17u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html
index 9a49c82f..2b4bf680 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/join-split-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>join</span><wbr></wbr><span>Split</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">100000u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="join-split-size.html">joinSplitSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--join-split-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">100000u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html
index 5fa1b10e..cf05f2bf 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/key2.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>key2</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="key2.html">key2</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--key2</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html
index 3026932b..881ba119 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/left-most-interval.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>left</span><wbr></wbr><span>Most</span><wbr></wbr><span><span>Interval</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p><p class="paragraph">Default: <code class="lang-kotlin">32</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="left-most-interval.html">leftMostInterval</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--left-most-interval</code></p><p class="paragraph">Default: <code class="lang-kotlin">32</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html
index d792169e..0c74a3b9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/length-ratio-threshold.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>length</span><wbr></wbr><span>Ratio</span><wbr></wbr><span><span>Threshold</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="length-ratio-threshold.html">lengthRatioThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--length-ratio-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html
index 1e555217..46d53d60 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/load-balancing.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>load</span><wbr></wbr><span><span>Balancing</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="load-balancing.html">loadBalancing</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--load-balancing</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html
index 47e84904..2d970bef 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-extend.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>log</span><wbr></wbr><span><span>Extend</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-extend.html">logExtend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-extend</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html
index a3a3e34a..6fc83d15 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-query.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>log</span><wbr></wbr><span><span>Query</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-query.html">logQuery</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-query</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html
index 4eba316a..506875e5 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/log-subject.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>log</span><wbr></wbr><span><span>Subject</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="log-subject.html">logSubject</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--log-subject</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html
index 25a0a40b..888011a3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/map-any.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>map</span><wbr></wbr><span><span>Any</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="map-any.html">mapAny</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--mapany</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html
index 479d09bf..7c77f20a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-cells.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>max</span><wbr></wbr><span><span>Cells</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p><p class="paragraph">Default: <code class="lang-kotlin">10000000u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-cells.html">maxCells</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-cells</code></p><p class="paragraph">Default: <code class="lang-kotlin">10000000u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html
index c887cd75..9003e98b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-indirection.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>max</span><wbr></wbr><span><span>Indirection</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-indirection.html">maxIndirection</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-indirection</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html
index a5f459bb..a50b92a1 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-motif-len.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>max</span><wbr></wbr><span>Motif</span><wbr></wbr><span><span>Len</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">30</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-motif-len.html">maxMotifLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-motif-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">30</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html
index 32ee4602..fef02377 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/max-swipe-dp.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>max</span><wbr></wbr><span>Swipe</span><wbr></wbr><span><span>Dp</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p><p class="paragraph">Default: <code class="lang-kotlin">1000000</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="max-swipe-dp.html">maxSwipeDp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--max-swipe-dp</code></p><p class="paragraph">Default: <code class="lang-kotlin">1000000</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html
index 2366c9c8..f363d345 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/maximum-seed-frequency.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>maximum</span><wbr></wbr><span>Seed</span><wbr></wbr><span><span>Frequency</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Maximum seed frequency.</p><p class="paragraph">Flag: <code class="lang-kotlin">--seed-freq</code></p><p class="paragraph">Default = <code class="lang-kotlin">-15.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="maximum-seed-frequency.html">maximumSeedFrequency</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Maximum seed frequency.</p><p class="paragraph">Flag: <code class="lang-kotlin">--seed-freq</code></p><p class="paragraph">Default = <code class="lang-kotlin">-15.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html
index 993c38ad..1469afc3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-chunk-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>mcl</span><wbr></wbr><span>Chunk</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL chunk size per thread.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-chunk-size</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-chunk-size.html">mclChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL chunk size per thread.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-chunk-size</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html
index 31d25f41..dfa6793a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-expansion.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>mcl</span><wbr></wbr><span><span>Expansion</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL expansion coefficient.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-expansion</code></p><p class="paragraph">Default: <code class="lang-kotlin">2</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-expansion.html">mclExpansion</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL expansion coefficient.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-expansion</code></p><p class="paragraph">Default: <code class="lang-kotlin">2</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html
index 6ea713bb..45363f35 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-inflation.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>mcl</span><wbr></wbr><span><span>Inflation</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">MCL inflation coefficient.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-inflation</code></p><p class="paragraph">Default: <code class="lang-kotlin">2.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-inflation.html">mclInflation</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">MCL inflation coefficient.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-inflation</code></p><p class="paragraph">Default: <code class="lang-kotlin">2.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html
index 18a6ab1d..991b14a9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-max-iterations.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>mcl</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Iterations</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL maximum iterations.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-max-iterations</code></p><p class="paragraph">Default: <code class="lang-kotlin">100</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-max-iterations.html">mclMaxIterations</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">MCL maximum iterations.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-max-iterations</code></p><p class="paragraph">Default: <code class="lang-kotlin">100</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html
index 7e8ad7b2..0dbc46aa 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-non-symmetric.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>mcl</span><wbr></wbr><span>Non</span><wbr></wbr><span><span>Symmetric</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-nonsymmetric</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-non-symmetric.html">mclNonSymmetric</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Do not symmetrize the transition matrix before clustering.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-nonsymmetric</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html
index b5fe9038..7bae8541 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-sparsity-switch.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>mcl</span><wbr></wbr><span>Sparsity</span><wbr></wbr><span><span>Switch</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">MCL switch to sparse matrix computation.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-sparsity-switch</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.8</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-sparsity-switch.html">mclSparsitySwitch</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">MCL switch to sparse matrix computation.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-sparsity-switch</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.8</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html
index e55de892..9ba53597 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/mcl-stats.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>mcl</span><wbr></wbr><span><span>Stats</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Some stats about the connected components in MCL.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-stats</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="mcl-stats.html">mclStats</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Some stats about the connected components in MCL.</p><p class="paragraph">Flag: <code class="lang-kotlin">--mcl-stats</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html
index b09c2548..ebaf72d9 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/memory-intervals.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>memory</span><wbr></wbr><span><span>Intervals</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p><p class="paragraph">Default: <code class="lang-kotlin">2</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="memory-intervals.html">memoryIntervals</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--memory-intervals</code></p><p class="paragraph">Default: <code class="lang-kotlin">2</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html
index 0def7543..a6c7a25a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-band-overlap.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>min</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Overlap</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-band-overlap.html">minBandOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-band-overlap</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html
index 65a3e2d5..b16fa2e3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-len-ratio.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>min</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Ratio</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-len-ratio.html">minLenRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-len-ratio</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html
index 26ad621c..8d5ef8e8 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-realign-overhang.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>min</span><wbr></wbr><span>Realign</span><wbr></wbr><span><span>Overhang</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p><p class="paragraph">Default: <code class="lang-kotlin">30</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-realign-overhang.html">minRealignOverhang</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min-realign-overhang</code></p><p class="paragraph">Default: <code class="lang-kotlin">30</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html
index b16c24a9..d4ce72c1 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/min-task-trace-pts.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>min</span><wbr></wbr><span>Task</span><wbr></wbr><span>Trace</span><wbr></wbr><span><span>Pts</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p><p class="paragraph">Default: <code class="lang-kotlin">1024</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="min-task-trace-pts.html">minTaskTracePts</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--min_task_trace_pts</code></p><p class="paragraph">Default: <code class="lang-kotlin">1024</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html
index 39adc3f3..193039a5 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/minimizer-window.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>minimizer</span><wbr></wbr><span><span>Window</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="minimizer-window.html">minimizerWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--minimizer-window</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html
index b6ae0a74..33d72d70 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/motif-mask-file.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>motif</span><wbr></wbr><span>Mask</span><wbr></wbr><span><span>File</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--motif-mask-file</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="motif-mask-file.html">motifMaskFile</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--motif-mask-file</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html
index 6ae06e92..1f4c9730 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-cov.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>narrow</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Cov</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-cov.html">narrowBandCov</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-cov</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html
index 58d91323..1dd43451 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/narrow-band-factor.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>narrow</span><wbr></wbr><span>Band</span><wbr></wbr><span><span>Factor</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="narrow-band-factor.html">narrowBandFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--narrow-band-factor</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html
index fe42ece7..e70c2d26 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighborhood-score.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>neighborhood</span><wbr></wbr><span><span>Score</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighborhood-score.html">neighborhoodScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--neighborhood-score</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html
index d763bf50..b5a7444b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/neighbors.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>neighbors</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--neighbors</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="neighbors.html">neighbors</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--neighbors</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html
index e5efa9a2..fa279240 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-chaining-merge-h-s-ps.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span>Chaining</span><wbr></wbr><span>Merge</span><wbr></wbr><span><span>HSPs</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-chaining-merge-h-s-ps.html">noChainingMergeHSPs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no_chaining_merge_hsps</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html
index 356eb494..04a00ab4 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-dict.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span><span>Dict</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-dict.html">noDict</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-dict</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html
index d27cad95..d57deadd 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-forward-fp.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span>Forward</span><wbr></wbr><span><span>Fp</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-forward-fp.html">noForwardFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-forward-fp</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html
index 4255c527..dd758cfe 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-log-file.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span>Log</span><wbr></wbr><span><span>File</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-log-file.html">noLogFile</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-logfile</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html
index 4886804c..c78d7c03 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reextend.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span><span>Reextend</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reextend.html">noReextend</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-reextend</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html
index 785e5507..2e410343 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-ref-masking.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span>Ref</span><wbr></wbr><span><span>Masking</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-ref-masking.html">noRefMasking</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-ref-masking</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html
index 2c4abeae..bb02e12b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-reorder.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span><span>Reorder</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-reorder.html">noReorder</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-reorder</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html
index 8d90e556..48517078 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no-swipe-realign.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no</span><wbr></wbr><span>Swipe</span><wbr></wbr><span><span>Realign</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no-swipe-realign.html">noSwipeRealign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no-swipe-realign</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html
index 8a605b6d..f518dd95 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/no8-bit-extension.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>no8Bit</span><wbr></wbr><span><span>Extension</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="no8-bit-extension.html">no8BitExtension</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--no_8bit_extension</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html
index 26915b02..7ae7fb3a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/oid-list.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>oid</span><wbr></wbr><span><span>List</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="oid-list.html">oidList</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--oid-list</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html
index 3c153ee0..83565428 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-fp.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>output</span><wbr></wbr><span><span>Fp</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-fp.html">outputFp</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--output-fp</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html
index 9f3c29ca..62cbcd0a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/output-hits.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>output</span><wbr></wbr><span><span>Hits</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="output-hits.html">outputHits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--output-hits</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html
index 0ed0290f..9ad426f3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-align.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>p</span><wbr></wbr><span><span>Align</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-align.html">pAlign</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--palign</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html
index 840e36ed..f19a1b4b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/p-best.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>p</span><wbr></wbr><span><span>Best</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.05</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="p-best.html">pBest</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--p_best</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.05</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html
index bc640729..7384eae1 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/path-cutoff.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>path</span><wbr></wbr><span><span>Cutoff</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.92</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="path-cutoff.html">pathCutoff</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--path-cutoff</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.92</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html
index 4564882d..ce2261bf 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/pipeline-short.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>pipeline</span><wbr></wbr><span><span>Short</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="pipeline-short.html">pipelineShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--pipeline-short</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html
index faa18d19..6e6f15d5 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/prefix-scan.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>prefix</span><wbr></wbr><span><span>Scan</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="prefix-scan.html">prefixScan</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--prefix-scan</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html
index ee753726..dce2f66b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-count.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>query</span><wbr></wbr><span><span>Count</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p><p class="paragraph">Default: <code class="lang-kotlin">1</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-count.html">queryCount</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-count</code></p><p class="paragraph">Default: <code class="lang-kotlin">1</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html
index f56468ca..0e3b551f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-match-distance-threshold.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>query</span><wbr></wbr><span>Match</span><wbr></wbr><span>Distance</span><wbr></wbr><span><span>Threshold</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-match-distance-threshold.html">queryMatchDistanceThreshold</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-match-distance-threshold</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html
index 75c63692..2b139d7a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/query-memory.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>query</span><wbr></wbr><span><span>Memory</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="query-memory.html">queryMemory</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--query-memory</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html
index 058b4a36..6c595292 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-bits.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>radix</span><wbr></wbr><span><span>Bits</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p><p class="paragraph">Default: <code class="lang-kotlin">8u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-bits.html">radixBits</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--radix-bits</code></p><p class="paragraph">Default: <code class="lang-kotlin">8u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html
index 25627554..c0e8dae7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/radix-cluster-buffered.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>radix</span><wbr></wbr><span>Cluster</span><wbr></wbr><span><span>Buffered</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="radix-cluster-buffered.html">radixClusterBuffered</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--radix-cluster-buffered</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html
index 6d3d0cfe..c7a528b2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rank-factor.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>rank</span><wbr></wbr><span><span>Factor</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rank-factor.html">rankFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--rank-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html
index cb322696..f12acca0 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-cutoff-bit-score.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>ranking</span><wbr></wbr><span>Cutoff</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p><p class="paragraph">Default: <code class="lang-kotlin">25.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-cutoff-bit-score.html">rankingCutoffBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ranking-cutoff-bitscore</code></p><p class="paragraph">Default: <code class="lang-kotlin">25.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html
index e4a60371..44281448 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ranking-score-drop-factor.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>ranking</span><wbr></wbr><span>Score</span><wbr></wbr><span>Drop</span><wbr></wbr><span><span>Factor</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.95</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ranking-score-drop-factor.html">rankingScoreDropFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-drop-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.95</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html
index 48173826..420bbc84 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/raw.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>raw</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="raw.html">raw</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--raw</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html
index 41695947..774f17bf 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-max.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>reassign</span><wbr></wbr><span><span>Max</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-max.html">reassignMax</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-max</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html
index 44069486..e03a34f7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-overlap.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>reassign</span><wbr></wbr><span><span>Overlap</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.3</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-overlap.html">reassignOverlap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-overlap</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.3</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html
index 6c55a0ef..e0ad0a97 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reassign-ratio.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>reassign</span><wbr></wbr><span><span>Ratio</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reassign-ratio.html">reassignRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reassign-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html
index 428f07ed..a22eb2ad 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/relaxed-e-value-factor.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>relaxed</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Factor</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="relaxed-e-value-factor.html">relaxedEValueFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--relaxed-evalue-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html
index 81922e17..c40fd8ac 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/resume.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>resume</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--resume</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="resume.html">resume</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></div><p class="paragraph">TODO: this flag appears to be unused.</p><p class="paragraph">Flag: <code class="lang-kotlin">--resume</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html
index 2b948a51..0b272039 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/reverse.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>reverse</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="reverse.html">reverse</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--reverse</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html
index 39af87b1..f6f8334e 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/rho.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>rho</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.99</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="rho.html">rho</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--rho</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.99</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html
index 72e5beb6..9f8d1ac8 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-estimate-factor.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>score</span><wbr></wbr><span>Estimate</span><wbr></wbr><span><span>Factor</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-estimate-factor.html">scoreEstimateFactor</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-estimate-factor</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html
index 6f46fac2..eaf05096 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/score-ratio.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>score</span><wbr></wbr><span><span>Ratio</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.9</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="score-ratio.html">scoreRatio</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--score-ratio</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.9</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html
index 589586b7..e2f9f6b3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-hit-density.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>seed</span><wbr></wbr><span>Hit</span><wbr></wbr><span><span>Density</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-hit-density.html">seedHitDensity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--seed-hit-density</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html
index 07d2930d..a125f59b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/seed-weight.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>seed</span><wbr></wbr><span><span>Weight</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p><p class="paragraph">Default: <code class="lang-kotlin">7u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="seed-weight.html">seedWeight</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--seed-weight</code> | <code class="lang-kotlin">-w</code></p><p class="paragraph">Default: <code class="lang-kotlin">7u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html
index df3b2e7e..d8a32f9c 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/self.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>self</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="self.html">self</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--self</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html
index 487b584c..58ad5abe 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-max-len.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>short</span><wbr></wbr><span>Query</span><wbr></wbr><span>Max</span><wbr></wbr><span><span>Len</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">60</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-max-len.html">shortQueryMaxLen</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-max-len</code></p><p class="paragraph">Default: <code class="lang-kotlin">60</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html
index e7ce847a..b8fab839 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-query-ungapped-bit-score.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>short</span><wbr></wbr><span>Query</span><wbr></wbr><span>Ungapped</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>Score</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p><p class="paragraph">Default: <code class="lang-kotlin">25.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-query-ungapped-bit-score.html">shortQueryUngappedBitScore</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-query-ungapped-bitscore</code></p><p class="paragraph">Default: <code class="lang-kotlin">25.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html
index 532e2017..c868e5b3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/short-seq-i-ds.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>short</span><wbr></wbr><span>Seq</span><wbr></wbr><span><span>IDs</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="short-seq-i-ds.html">shortSeqIDs</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--short-seqids</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html
index f3e5d782..875ce5bf 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/simple-freq.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>simple</span><wbr></wbr><span><span>Freq</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="simple-freq.html">simpleFreq</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--simple-freq</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html
index 0ac87ce5..81f5e71a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sketch-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>sketch</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sketch-size.html">sketchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sketch-size</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html
index f35e85a8..f30ad9b6 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/sort-join.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>sort</span><wbr></wbr><span><span>Join</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="sort-join.html">sortJoin</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sort-join</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html
index 0302ca1e..d2cd8eff 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/space-penalty.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>space</span><wbr></wbr><span><span>Penalty</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="space-penalty.html">spacePenalty</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--space-penalty</code></p><p class="paragraph">Default: <code class="lang-kotlin">0.5</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html
index 7a32bfc2..8ab8a1a5 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/store-query-quality.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>store</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Quality</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="store-query-quality.html">storeQueryQuality</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--store-query-quality</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html
index 1a82dc89..f3276f74 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/strict-g-v-c.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>strict</span><wbr></wbr><span><span>GVC</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="strict-g-v-c.html">strictGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--strict-gvc</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html
index 19fa449f..69d35331 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/superblock.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>superblock</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p><p class="paragraph">Default: <code class="lang-kotlin">128</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="superblock.html">superblock</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--superblock</code></p><p class="paragraph">Default: <code class="lang-kotlin">128</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html
index b25b8b7b..d89bd5ad 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-chunk-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>swipe</span><wbr></wbr><span>Chunk</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">256u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-chunk-size.html">swipeChunkSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-chunk-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">256u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html
index 42e4dbee..4acb3b7c 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/swipe-task-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>swipe</span><wbr></wbr><span>Task</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">100000000</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="swipe-task-size.html">swipeTaskSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--swipe-task-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">100000000</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html
index bd13a158..30e52b51 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-max-repeat-offset.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>tantan</span><wbr></wbr><span>Max</span><wbr></wbr><span>Repeat</span><wbr></wbr><span><span>Offset</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Maximum tandem repeat period to consider (50)</p><p class="paragraph">Flag: <code class="lang-kotlin">--tantan-maxRepeatOffset</code> // TODO: the caps are in the diamond cli source, are flag strings case sensitive?</p><p class="paragraph">Default: <code class="lang-kotlin">15</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-max-repeat-offset.html">tantanMaxRepeatOffset</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Maximum tandem repeat period to consider (50)</p><p class="paragraph">Flag: <code class="lang-kotlin">--tantan-maxRepeatOffset</code> // TODO: the caps are in the diamond cli source, are flag strings case sensitive?</p><p class="paragraph">Default: <code class="lang-kotlin">15</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html
index 775b8322..ee4f0231 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tantan-ungapped.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>tantan</span><wbr></wbr><span><span>Ungapped</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Use tantan masking in ungapped mode</p><p class="paragraph">Flag: <code class="lang-kotlin">--tantan-ungapped</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tantan-ungapped.html">tantanUngapped</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Use tantan masking in ungapped mode</p><p class="paragraph">Flag: <code class="lang-kotlin">--tantan-ungapped</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html
index 40f3a652..cc774a36 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-bias.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>target</span><wbr></wbr><span><span>Bias</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-bias.html">targetBias</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target-bias</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html
index bb4c53f8..b0acb382 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-fetch-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>target</span><wbr></wbr><span>Fetch</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Number of target sequences to fetch for seed extension.</p><p class="paragraph">Flag: <code class="lang-kotlin">--target-fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">4u</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-fetch-size.html">targetFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Number of target sequences to fetch for seed extension.</p><p class="paragraph">Flag: <code class="lang-kotlin">--target-fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">4u</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html
index aa153b2a..459de4c7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-hard-cap.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>target</span><wbr></wbr><span>Hard</span><wbr></wbr><span><span>Cap</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-hard-cap.html">targetHardCap</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target_hard_cap</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html
index 929b279d..94081ac2 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/target-parallel-verbosity.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>target</span><wbr></wbr><span>Parallel</span><wbr></wbr><span><span>Verbosity</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="target-parallel-verbosity.html">targetParallelVerbosity</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--target-parallel-verbosity</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html
index cc9b9eee..bdcf15da 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tile-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>tile</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">1024</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tile-size.html">tileSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-int/index.html">UInt</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tile-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">1024</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html
index 26f690f5..112b3914 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/timeout.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>timeout</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="timeout.html">timeout</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--timeout</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html
index bb54f660..fd072388 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/trace-pt-fetch-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>trace</span><wbr></wbr><span>Pt</span><wbr></wbr><span>Fetch</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">10e9</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="trace-pt-fetch-size.html">tracePtFetchSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--trace-pt-fetch-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">10e9</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html
index e29d5944..9ab93224 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/transcript-len-estimate.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>transcript</span><wbr></wbr><span>Len</span><wbr></wbr><span><span>Estimate</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="transcript-len-estimate.html">transcriptLenEstimate</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--transcript-len-estimate</code></p><p class="paragraph">Default: <code class="lang-kotlin">1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html
index 3d8861ae..9b46beb3 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tree.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>tree</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tree.html">tree</a><span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html">Path</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tree</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html
index b2037ae1..8c3d5140 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/tsv-read-size.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>tsv</span><wbr></wbr><span>Read</span><wbr></wbr><span><span>Size</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">1073741824</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="tsv-read-size.html">tsvReadSize</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-long/index.html">Long</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--tsv-read-size</code></p><p class="paragraph">Default: <code class="lang-kotlin">1073741824</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html
index 87d5af1f..a538888d 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/type.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span><span>type</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="type.html">type</a><span class="token operator">: </span><a href="../-benchmark-type/index.html">BenchmarkType</a></div><p class="paragraph">TODO: seems to only be used by benchmark?</p><p class="paragraph">Flag: <code class="lang-kotlin">--type</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="type.html">type</a><span class="token operator">: </span><a href="../-benchmark-type/index.html">BenchmarkType</a></div><p class="paragraph">TODO: seems to only be used by benchmark?</p><p class="paragraph">Flag: <code class="lang-kotlin">--type</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html
index 68f261fe..c478b702 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value-short.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>ungapped</span><wbr></wbr><span>EValue</span><wbr></wbr><span><span>Short</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value-short.html">ungappedEValueShort</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue-short</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html
index 76cf6972..277101d5 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-e-value.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>ungapped</span><wbr></wbr><span><span>EValue</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-e-value.html">ungappedEValue</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-double/index.html">Double</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-evalue</code></p><p class="paragraph">Default: <code class="lang-kotlin">-1.0</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html
index 21509e4e..326d9fd8 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/ungapped-window.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>ungapped</span><wbr></wbr><span><span>Window</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">48</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="ungapped-window.html">ungappedWindow</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-int/index.html">Int</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--ungapped-window</code></p><p class="paragraph">Default: <code class="lang-kotlin">48</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html
index d8fa97ca..6715451e 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-dist.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span><span>Dist</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../-distribution-type/index.html">DistributionType</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-dist.html">upGmaDist</a><span class="token operator">: </span><a href="../-distribution-type/index.html">DistributionType</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-dist</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html
index 51e93326..c298a32e 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-edge-limit.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span>Edge</span><wbr></wbr><span><span>Limit</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p><p class="paragraph">Default: <code class="lang-kotlin">10000000</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-edge-limit.html">upGmaEdgeLimit</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-u-long/index.html">ULong</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-edge-limit</code></p><p class="paragraph">Default: <code class="lang-kotlin">10000000</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html
index dd859e74..e7a181b4 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/up-gma-input.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>up</span><wbr></wbr><span>Gma</span><wbr></wbr><span><span>Input</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../-input-type/index.html">InputType</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="up-gma-input.html">upGmaInput</a><span class="token operator">: </span><a href="../-input-type/index.html">InputType</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--upgma-input</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html
index caf209b4..ec55f165 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-dataset-field.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>use</span><wbr></wbr><span>Dataset</span><wbr></wbr><span><span>Field</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-dataset-field.html">useDatasetField</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--use-dataset-field</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html
index 557e70b4..a384805c 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/use-smith-waterman.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>use</span><wbr></wbr><span>Smith</span><wbr></wbr><span><span>Waterman</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="use-smith-waterman.html">useSmithWaterman</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--sw</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html
index 9ab16711..ab3570cd 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-hidden-option-container/weighted-g-v-c.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>weighted</span><wbr></wbr><span><span>GVC</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../org.veupathdb.lib.cli.diamond/-diamond-hidden/index.html"><span class="token annotation builtin">DiamondHidden</span></a></div></div><span class="token keyword">abstract </span><span class="token keyword">var </span><a href="weighted-g-v-c.html">weightedGVC</a><span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-boolean/index.html">Boolean</a></div><p class="paragraph">Flag: <code class="lang-kotlin">--weighted-gvc</code></p></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-output-format-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-output-format-option-container/index.html
index f83926ee..e98bafe8 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-output-format-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-output-format-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">OutputFormatOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Output</span><wbr></wbr><span>Format</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">OutputFormatOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-output-format-option-container-impl/index.html">OutputFormatOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">OutputFormatOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-cluster-realign/index.html">ClusterRealign</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-view-align-option-container/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-view-align-option-container/index.html
index 4a0af427..1966916f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-view-align-option-container/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond.opts/-view-align-option-container/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../index.html">org.veupathdb.lib.cli.diamond.opts</a><span class="delimiter">/</span><span class="current">ViewAlignOptionContainer</span></div>
   <div class="cover ">
     <h1 class="cover"><span>View</span><wbr></wbr><span>Align</span><wbr></wbr><span>Option</span><wbr></wbr><span><span>Container</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">ViewAlignOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/index.html">ViewAlignOptionContainerImpl</a></div></span></div><div></div></div></div></div></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">interface </span><a href="index.html">ViewAlignOptionContainer</a></div><h4 class="">Inheritors</h4><div class="table"><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-p/index.html">BlastP</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-x/index.html">BlastX</a></div></span></div><div></div></div></div><div class="table-row" data-filterable-current=":dokkaHtml/main" data-filterable-set=":dokkaHtml/main"><div class="main-subrow keyValue "><div class=""><span class="inline-flex"><div><a href="../../org.veupathdb.lib.cli.diamond.commands/-view/index.html">View</a></div></span></div><div></div></div></div></div></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-blast-n/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-blast-n/index.html
index ca805a9b..bcc5931f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-blast-n/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-blast-n/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">BlastN</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Blast</span><wbr></wbr><span><span>N</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">BlastN</a></div></div><p class="paragraph">Align DNA query sequences against a DNA reference database.</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">BlastN</a></div></div><p class="paragraph">Align DNA query sequences against a DNA reference database.</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-composition/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-composition/index.html
index b1a277e2..d8e2b2ea 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-composition/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-composition/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Composition</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Composition</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Composition</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Composition</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-compute-medoids/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-compute-medoids/index.html
index 74616839..4eb15f6b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-compute-medoids/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-compute-medoids/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">ComputeMedoids</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Compute</span><wbr></wbr><span><span>Medoids</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">ComputeMedoids</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">ComputeMedoids</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-cut/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-cut/index.html
index 2e245f1f..551ec9e1 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-cut/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-cut/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Cut</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Cut</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Cut</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Cut</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-d-b-stats/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-d-b-stats/index.html
index adb9b034..7fd43279 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-d-b-stats/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-d-b-stats/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">DBStats</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>DBStats</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">DBStats</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">DBStats</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fast-q2-fast-a/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fast-q2-fast-a/index.html
index 4f66a9f2..679bee57 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fast-q2-fast-a/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fast-q2-fast-a/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">FastQ2FastA</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Fast</span><wbr></wbr><span>Q2Fast</span><wbr></wbr><span><span>A</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">FastQ2FastA</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">FastQ2FastA</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fetch-seq/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fetch-seq/index.html
index ba724431..149ba9b7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fetch-seq/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-fetch-seq/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">FetchSeq</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Fetch</span><wbr></wbr><span><span>Seq</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">FetchSeq</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">FetchSeq</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-filter-blast-tab/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-filter-blast-tab/index.html
index 7aab41f2..6ee660b4 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-filter-blast-tab/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-filter-blast-tab/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">FilterBlastTab</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Filter</span><wbr></wbr><span>Blast</span><wbr></wbr><span><span>Tab</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">FilterBlastTab</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">FilterBlastTab</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-find-shapes/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-find-shapes/index.html
index 2402cc1a..fec23ada 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-find-shapes/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-find-shapes/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">FindShapes</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Find</span><wbr></wbr><span><span>Shapes</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">FindShapes</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">FindShapes</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-hash-seqs/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-hash-seqs/index.html
index f6e5e84b..77fb929c 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-hash-seqs/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-hash-seqs/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">HashSeqs</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Hash</span><wbr></wbr><span><span>Seqs</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">HashSeqs</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">HashSeqs</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-index-fast-a/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-index-fast-a/index.html
index 4d99c0ab..32f2812e 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-index-fast-a/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-index-fast-a/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">IndexFastA</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Index</span><wbr></wbr><span>Fast</span><wbr></wbr><span><span>A</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">IndexFastA</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">IndexFastA</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-join/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-join/index.html
index 743e1263..b9576b0b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-join/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-join/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Join</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Join</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Join</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Join</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-length-sort/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-length-sort/index.html
index 806bacb9..6dd96b6f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-length-sort/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-length-sort/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">LengthSort</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Length</span><wbr></wbr><span><span>Sort</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">LengthSort</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">LengthSort</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-list-seeds/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-list-seeds/index.html
index f43d60aa..aab46952 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-list-seeds/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-list-seeds/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">ListSeeds</span></div>
   <div class="cover ">
     <h1 class="cover"><span>List</span><wbr></wbr><span><span>Seeds</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">ListSeeds</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">ListSeeds</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mask/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mask/index.html
index df423e9a..a30433fd 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mask/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mask/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Mask</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Mask</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Mask</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Mask</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-model-seqs/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-model-seqs/index.html
index bfb764f5..2d544e51 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-model-seqs/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-model-seqs/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">ModelSeqs</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Model</span><wbr></wbr><span><span>Seqs</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">ModelSeqs</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">ModelSeqs</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mutate/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mutate/index.html
index 9ff662ea..04971a18 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mutate/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-mutate/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Mutate</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Mutate</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Mutate</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Mutate</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-r-o-c-i-d/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-r-o-c-i-d/index.html
index e0929cbf..a92fe671 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-r-o-c-i-d/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-r-o-c-i-d/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">ROCID</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>ROCID</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">ROCID</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">ROCID</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-random-seqs/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-random-seqs/index.html
index 5510e4fb..e7a50487 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-random-seqs/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-random-seqs/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">RandomSeqs</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Random</span><wbr></wbr><span><span>Seqs</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">RandomSeqs</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">RandomSeqs</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-read-sim/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-read-sim/index.html
index c94573a9..93d406df 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-read-sim/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-read-sim/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">ReadSim</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Read</span><wbr></wbr><span><span>Sim</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">ReadSim</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">ReadSim</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-reverse/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-reverse/index.html
index 40bbdc35..c9de6a4c 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-reverse/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-reverse/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Reverse</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Reverse</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Reverse</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Reverse</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-seed-stat/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-seed-stat/index.html
index fa8b1eb4..52801af7 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-seed-stat/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-seed-stat/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">SeedStat</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Seed</span><wbr></wbr><span><span>Stat</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">SeedStat</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">SeedStat</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-show-c-b-s/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-show-c-b-s/index.html
index 653f1509..ca1a165f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-show-c-b-s/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-show-c-b-s/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">ShowCBS</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Show</span><wbr></wbr><span><span>CBS</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">ShowCBS</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">ShowCBS</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-simulate-seqs/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-simulate-seqs/index.html
index 5fafe1be..3df6f07a 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-simulate-seqs/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-simulate-seqs/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">SimulateSeqs</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Simulate</span><wbr></wbr><span><span>Seqs</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">SimulateSeqs</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">SimulateSeqs</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-smith-waterman/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-smith-waterman/index.html
index 1f166204..d3646332 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-smith-waterman/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-smith-waterman/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">SmithWaterman</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Smith</span><wbr></wbr><span><span>Waterman</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">SmithWaterman</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">SmithWaterman</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-sort/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-sort/index.html
index f0fe425b..5516a28b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-sort/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-sort/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Sort</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Sort</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Sort</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Sort</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-split/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-split/index.html
index b4cd9d3a..b73fc495 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-split/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-split/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Split</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Split</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Split</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Split</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-translate/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-translate/index.html
index a0fdf195..a6928e67 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-translate/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-translate/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">Translate</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>Translate</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">Translate</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">Translate</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a-m-c/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a-m-c/index.html
index 05f4803d..aaa1a957 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a-m-c/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a-m-c/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">UpGMAMC</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Up</span><wbr></wbr><span><span>GMAMC</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">UpGMAMC</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">UpGMAMC</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a/index.html
index 332a7867..72f0b76d 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-up-g-m-a/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">UpGMA</span></div>
   <div class="cover ">
     <h1 class="cover"><span>Up</span><wbr></wbr><span><span>GMA</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">UpGMA</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">UpGMA</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-w-c/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-w-c/index.html
index eefe67b5..5e74f151 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-w-c/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/-w-c/index.html
@@ -66,7 +66,7 @@
   <div class="breadcrumbs"><a href="../../../../index.html">diamondcli</a><span class="delimiter">/</span><a href="../../index.html">org.veupathdb.lib.cli.diamond</a><span class="delimiter">/</span><a href="../index.html">DiamondCommand</a><span class="delimiter">/</span><span class="current">WC</span></div>
   <div class="cover ">
     <h1 class="cover"><span><span>WC</span></span></h1>
-    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="index.html">WC</a></div></div><p class="paragraph">???</p></div></div>
+    <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="index.html">WC</a></div></div><p class="paragraph">???</p></div></div>
   </div>
   <div class="tabbedcontent">
     <div class="tabs-section" tabs-section="tabs-section"><button class="section-tab" data-active="" data-togglable="CONSTRUCTOR,TYPE,PROPERTY,FUNCTION">Members</button></div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/index.html
index 9947354b..c4bde80f 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond-command/index.html
@@ -398,7 +398,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-random-seqs/index.html">RandomSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-random-seqs/index.html">RandomSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -413,7 +413,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-sort/index.html">Sort</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-sort/index.html">Sort</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -428,7 +428,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-d-b-stats/index.html">DBStats</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-d-b-stats/index.html">DBStats</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -443,7 +443,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-mask/index.html">Mask</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-mask/index.html">Mask</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -458,7 +458,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-fast-q2-fast-a/index.html">FastQ2FastA</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-fast-q2-fast-a/index.html">FastQ2FastA</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -473,7 +473,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-read-sim/index.html">ReadSim</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-read-sim/index.html">ReadSim</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -488,7 +488,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-seed-stat/index.html">SeedStat</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-seed-stat/index.html">SeedStat</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -503,7 +503,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-smith-waterman/index.html">SmithWaterman</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-smith-waterman/index.html">SmithWaterman</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -518,7 +518,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-translate/index.html">Translate</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-translate/index.html">Translate</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -533,7 +533,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-filter-blast-tab/index.html">FilterBlastTab</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-filter-blast-tab/index.html">FilterBlastTab</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -548,7 +548,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-show-c-b-s/index.html">ShowCBS</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-show-c-b-s/index.html">ShowCBS</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -563,7 +563,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-simulate-seqs/index.html">SimulateSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-simulate-seqs/index.html">SimulateSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -578,7 +578,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-split/index.html">Split</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-split/index.html">Split</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -593,7 +593,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-up-g-m-a/index.html">UpGMA</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-up-g-m-a/index.html">UpGMA</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -608,7 +608,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-up-g-m-a-m-c/index.html">UpGMAMC</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-up-g-m-a-m-c/index.html">UpGMAMC</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -623,7 +623,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-reverse/index.html">Reverse</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-reverse/index.html">Reverse</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -638,7 +638,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-compute-medoids/index.html">ComputeMedoids</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-compute-medoids/index.html">ComputeMedoids</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -653,7 +653,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-mutate/index.html">Mutate</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-mutate/index.html">Mutate</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -668,7 +668,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-r-o-c-i-d/index.html">ROCID</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-r-o-c-i-d/index.html">ROCID</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -683,7 +683,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-find-shapes/index.html">FindShapes</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-find-shapes/index.html">FindShapes</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -698,7 +698,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-composition/index.html">Composition</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-composition/index.html">Composition</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -713,7 +713,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-join/index.html">Join</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-join/index.html">Join</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -728,7 +728,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-hash-seqs/index.html">HashSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-hash-seqs/index.html">HashSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -743,7 +743,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-list-seeds/index.html">ListSeeds</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-list-seeds/index.html">ListSeeds</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -758,7 +758,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-index-fast-a/index.html">IndexFastA</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-index-fast-a/index.html">IndexFastA</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -773,7 +773,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-fetch-seq/index.html">FetchSeq</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-fetch-seq/index.html">FetchSeq</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -788,7 +788,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-blast-n/index.html">BlastN</a></div></div><div class="brief "><p class="paragraph">Align DNA query sequences against a DNA reference database.</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-blast-n/index.html">BlastN</a></div></div><div class="brief "><p class="paragraph">Align DNA query sequences against a DNA reference database.</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -803,7 +803,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-length-sort/index.html">LengthSort</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-length-sort/index.html">LengthSort</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -818,7 +818,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-w-c/index.html">WC</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-w-c/index.html">WC</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -833,7 +833,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-cut/index.html">Cut</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-cut/index.html">Cut</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
@@ -848,7 +848,7 @@ <h2 class="">Entries</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><a href="-model-seqs/index.html">ModelSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><a href="-model-seqs/index.html">ModelSeqs</a></div></div><div class="brief "><p class="paragraph">???</p></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/blast-n.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/blast-n.html
index 87131870..615c943b 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/blast-n.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/blast-n.html
@@ -67,7 +67,7 @@
   <div class="cover ">
     <h1 class="cover"><span>blast</span><wbr></wbr><span><span>N</span></span></h1>
   </div>
-  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><span data-unresolved-link="com.fasterxml.jackson.databind/JsonNode///PointingToDeclaration/">JsonNode</span></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/io/InputStream.html">InputStream</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></div></div>
+  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><span data-unresolved-link="com.fasterxml.jackson.databind/JsonNode///PointingToDeclaration/">JsonNode</span></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/io/InputStream.html">InputStream</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></div></div>
 </div>
       <div class="footer">
         <span class="go-to-top-icon"><a href="#content" id="go-to-top-link"></a></span><span>© 2024 Copyright</span><span
diff --git a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/index.html b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/index.html
index 0411fa05..7b537828 100644
--- a/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/index.html
+++ b/docs/dokka/v0.1.0/diamondcli/org.veupathdb.lib.cli.diamond/-diamond/index.html
@@ -83,7 +83,7 @@ <h2 class="">Functions</h2>
                   </span></span></div>
               <div>
                 <div class="title">
-                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><span data-unresolved-link="com.fasterxml.jackson.databind/JsonNode///PointingToDeclaration/">JsonNode</span></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/io/InputStream.html">InputStream</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></div></div>
+                  <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-dependent-content" data-active="" data-togglable=":dokkaHtml/main"><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><span data-unresolved-link="com.fasterxml.jackson.databind/JsonNode///PointingToDeclaration/">JsonNode</span></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://docs.oracle.com/javase/8/docs/api/java/io/InputStream.html">InputStream</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div><div class="symbol monospace"><div class="block"><div class="block"><span class="token annotation builtin">@</span><a href="../-diamond-extras/index.html"><span class="token annotation builtin">DiamondExtras</span></a></div></div><span class="token keyword">fun </span><a href="blast-n.html"><span class="token function">blastN</span></a><span class="token punctuation">(</span><span class="parameters "><span class="parameter ">json<span class="token operator">: </span><a href="https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-string/index.html">String</a></span></span><span class="token punctuation">)</span><span class="token operator">: </span><a href="../../org.veupathdb.lib.cli.diamond.commands/-blast-n/index.html">BlastN</a></div></div></div>
                 </div>
               </div>
             </div>
diff --git a/docs/dokka/v0.1.0/diamondcli/package-list b/docs/dokka/v0.1.0/diamondcli/package-list
index 6feceac9..e4d919cc 100644
--- a/docs/dokka/v0.1.0/diamondcli/package-list
+++ b/docs/dokka/v0.1.0/diamondcli/package-list
@@ -51,320 +51,6 @@ $dokka.location:org.veupathdb.lib.cli.diamond.commands/View///PointingToDeclarat
 $dokka.location:org.veupathdb.lib.cli.diamond.commands/View/forwardOnly/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.commands/-view/forward-only.html
 $dokka.location:org.veupathdb.lib.cli.diamond.commands/View/inputFile/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.commands/-view/input-file.html
 $dokka.location:org.veupathdb.lib.cli.diamond.commands/View/tool/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.commands/-view/tool.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl////PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/index.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl///PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/index.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/AdvancedGeneralOptionContainerImpl/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/-advanced-general-option-container-impl.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/fileBufferSize/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/file-buffer-size.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/ignoreWarnings/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/ignore-warnings.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/noParseSeqIDs/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-parse-seq-i-ds.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedGeneralOptionContainerImpl/noUnlink/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-general-option-container-impl/no-unlink.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl///PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/index.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/AdvancedQueryOptionContainerImpl/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/-advanced-query-option-container-impl.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/algo/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/algo.html
-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/AdvancedQueryOptionContainerImpl/alignLongReads/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-advanced-query-option-container-impl/align-long-reads.html
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-$dokka.location:org.veupathdb.lib.cli.diamond.opts.impl/ViewAlignOptionContainerImpl/daa/#/PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.impl/-view-align-option-container-impl/daa.html
 $dokka.location:org.veupathdb.lib.cli.diamond.opts.output_format////PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/index.html
 $dokka.location:org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormat///PointingToDeclaration/diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format/index.html
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@@ -1174,7 +860,6 @@ $dokka.location:org.veupathdb.lib.cli.diamond/DiamondHidden///PointingToDeclarat
 org.veupathdb.lib.cli.diamond
 org.veupathdb.lib.cli.diamond.commands
 org.veupathdb.lib.cli.diamond.opts
-org.veupathdb.lib.cli.diamond.opts.impl
 org.veupathdb.lib.cli.diamond.opts.output_format
 org.veupathdb.lib.cli.diamond.util
 
diff --git a/docs/dokka/v0.1.0/index.html b/docs/dokka/v0.1.0/index.html
index a00dc62a..1aeb51e6 100644
--- a/docs/dokka/v0.1.0/index.html
+++ b/docs/dokka/v0.1.0/index.html
@@ -122,24 +122,6 @@ <h2 class="">Packages</h2>
         <div></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-sequence-length/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span>Sequence</span><wbr></wbr><span><span>Length</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-sequence-i-d/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Sequence</span><wbr></wbr><span><span>ID</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-all-subject-sequence-i-ds/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>All</span><wbr></wbr><span>Subject</span><wbr></wbr><span>Sequence</span><wbr></wbr><span><span>IDs</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-alignment-end/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span>Alignment</span><wbr></wbr><span><span>End</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-alignment-start/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Alignment</span><wbr></wbr><span><span>Start</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-alignment-end/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Alignment</span><wbr></wbr><span><span>End</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-aligned-subject-sequence/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Aligned</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>Sequence</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-raw-score/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Raw</span><wbr></wbr><span><span>Score</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-alignment-length/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Alignment</span><wbr></wbr><span><span>Length</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-percent-identical-matches/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Percent</span><wbr></wbr><span>Identical</span><wbr></wbr><span><span>Matches</span></span></span></span></a></div>
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-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-25" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.IdenticalMatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-25" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.IdenticalMatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-identical-matches/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Identical</span><wbr></wbr><span><span>Matches</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-26" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.Mismatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-26" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.Mismatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-mismatches/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span><span>Mismatches</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-27" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.PositiveScoringMatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-27" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.PositiveScoringMatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-positive-scoring-matches/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Positive</span><wbr></wbr><span>Scoring</span><wbr></wbr><span><span>Matches</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-28" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.GapOpenings///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-28" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.GapOpenings///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-gap-openings/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Gap</span><wbr></wbr><span><span>Openings</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-29" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.TotalGaps///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-29" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.TotalGaps///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-total-gaps/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Total</span><wbr></wbr><span><span>Gaps</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-30" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.PercentPositiveScoringMatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-30" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.PercentPositiveScoringMatches///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-percent-positive-scoring-matches/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Percent</span><wbr></wbr><span>Positive</span><wbr></wbr><span>Scoring</span><wbr></wbr><span><span>Matches</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-31" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.Frames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-31" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.Frames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-frames/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span><span>Frames</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-32" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryFrame///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-32" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryFrame///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-frame/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span><span>Frame</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-33" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectFrame///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-33" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectFrame///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-frame/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span><span>Frame</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-34" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.BlastTracebackOperations///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-34" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.BlastTracebackOperations///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-blast-traceback-operations/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Blast</span><wbr></wbr><span>Traceback</span><wbr></wbr><span><span>Operations</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-35" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectTaxonomyIDs///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-35" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectTaxonomyIDs///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-taxonomy-i-ds/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Taxonomy</span><wbr></wbr><span><span>IDs</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-36" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectScientificNames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-36" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectScientificNames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-scientific-names/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Scientific</span><wbr></wbr><span><span>Names</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-37" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectCommonNames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-37" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectCommonNames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-common-names/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Common</span><wbr></wbr><span><span>Names</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-38" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectBlastNames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-38" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectBlastNames///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-blast-names/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Blast</span><wbr></wbr><span><span>Names</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-39" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectSuperKingdoms///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-39" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectSuperKingdoms///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-super-kingdoms/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Super</span><wbr></wbr><span><span>Kingdoms</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-40" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectTitle///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-40" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectTitle///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-title/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span><span>Title</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-41" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.AllSubjectTitles///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-41" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.AllSubjectTitles///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-all-subject-titles/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>All</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>Titles</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-42" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectStrand///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-42" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectStrand///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-strand/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span><span>Strand</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-43" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryCoveragePerSubject///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-43" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryCoveragePerSubject///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-coverage-per-subject/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span>Coverage</span><wbr></wbr><span>Per</span><wbr></wbr><span><span>Subject</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-44" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryCoveragePerHSP///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-44" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryCoveragePerHSP///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-coverage-per-h-s-p/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span>Coverage</span><wbr></wbr><span>Per</span><wbr></wbr><span><span>HSP</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-45" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryCoveragePerUniqueSubject///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-45" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryCoveragePerUniqueSubject///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-coverage-per-unique-subject/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span>Coverage</span><wbr></wbr><span>Per</span><wbr></wbr><span>Unique</span><wbr></wbr><span><span>Subject</span></span></span></span></a></div>
       </div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-title/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span><span>Title</span></span></span></span></a></div>
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+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-47" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SWDiff///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-s-w-diff/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span><span>SWDiff</span></span></span></span></a></div>
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+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-48" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.Time///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-time/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span><span>Time</span></span></span></span></a></div>
       </div>
-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-49" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.FullSubjectSequence///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-49" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.FullSubjectSequence///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-full-subject-sequence/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Full</span><wbr></wbr><span>Subject</span><wbr></wbr><span><span>Sequence</span></span></span></span></a></div>
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+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-50" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.AlignedQueryQualityValues///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-aligned-query-quality-values/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Aligned</span><wbr></wbr><span>Query</span><wbr></wbr><span>Quality</span><wbr></wbr><span><span>Values</span></span></span></span></a></div>
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-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-51" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryNum///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-51" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QueryNum///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-num/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span><span>Num</span></span></span></span></a></div>
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+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-52" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectNum///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-num/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span><span>Num</span></span></span></span></a></div>
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+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-53" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectCoveragePerHSP///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-coverage-per-h-s-p/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Coverage</span><wbr></wbr><span>Per</span><wbr></wbr><span><span>HSP</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-full-query-quality-values/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Full</span><wbr></wbr><span>Query</span><wbr></wbr><span>Quality</span><wbr></wbr><span><span>Values</span></span></span></span></a></div>
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-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-55" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.FullQuerySequence///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-full-query-sequence/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Full</span><wbr></wbr><span>Query</span><wbr></wbr><span><span>Sequence</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-sequence-gapped/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span>Sequence</span><wbr></wbr><span><span>Gapped</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-sequence-gapped/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span>Sequence</span><wbr></wbr><span><span>Gapped</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-strand/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span><span>Strand</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-c-i-g-a-r/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span><span>CIGAR</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-kingdoms/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span><span>Kingdoms</span></span></span></span></a></div>
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+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-61" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.SubjectPhylums///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-subject-phylums/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Subject</span><wbr></wbr><span><span>Phylums</span></span></span></span></a></div>
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-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-62" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.UngappedScore///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-62" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.UngappedScore///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-ungapped-score/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Ungapped</span><wbr></wbr><span><span>Score</span></span></span></span></a></div>
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+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-63" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.FullQuerySequenceOfMate///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-full-query-sequence-of-mate/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Full</span><wbr></wbr><span>Query</span><wbr></wbr><span>Sequence</span><wbr></wbr><span>Of</span><wbr></wbr><span><span>Mate</span></span></span></span></a></div>
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-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-64" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QuerySequenceTranslated///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-64" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.QuerySequenceTranslated///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-query-sequence-translated/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Query</span><wbr></wbr><span>Sequence</span><wbr></wbr><span><span>Translated</span></span></span></span></a></div>
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-      <div class="sideMenuPart" id="diamondcli-nav-submenu-4-2-65" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.ReducedMatchBitString///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
+      <div class="sideMenuPart" id="diamondcli-nav-submenu-3-2-65" pageId="diamondcli::org.veupathdb.lib.cli.diamond.opts.output_format/BlastTabFormatField.ReducedMatchBitString///PointingToDeclaration/{&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;:{&quot;key&quot;:&quot;org.jetbrains.dokka.links.EnumEntryDRIExtra&quot;}}/769193423">
         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-reduced-match-bit-string/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Reduced</span><wbr></wbr><span>Match</span><wbr></wbr><span>Bit</span><wbr></wbr><span><span>String</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-blast-tab-format-field/-normalized-bit-score-semiglobal/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span>Normalized</span><wbr></wbr><span>Bit</span><wbr></wbr><span>Score</span><wbr></wbr><span><span>Semiglobal</span></span></span></span></a></div>
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         <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-output-format/-taxon/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon enum-class-kt"></span><span class="nav-link-child"><span><span>Taxon</span></span></span></span></a></div>
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       <div class="overview"><a href="diamondcli/org.veupathdb.lib.cli.diamond.opts.output_format/-output-format-options/index.html"><span class="nav-link-grid"><span class="nav-link-child nav-icon interface-kt"></span><span class="nav-link-child"><span>Output</span><wbr></wbr><span>Format</span><wbr></wbr><span><span>Options</span></span></span></span></a></div>
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-  <div class="sideMenuPart" id="diamondcli-nav-submenu-5" pageId="diamondcli::org.veupathdb.lib.cli.diamond.util////PointingToDeclaration//769193423">
-    <div class="overview"><span class="navButton" onclick="document.getElementById(&quot;diamondcli-nav-submenu-5&quot;).classList.toggle(&quot;hidden&quot;);"><span class="navButtonContent"></span></span><a href="diamondcli/org.veupathdb.lib.cli.diamond.util/index.html"><span>org.</span><wbr></wbr><span>veupathdb.</span><wbr></wbr><span>lib.</span><wbr></wbr><span>cli.</span><wbr></wbr><span>diamond.</span><wbr></wbr><span>util</span></a></div>
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diff --git a/docs/dokka/v0.1.0/scripts/pages.json b/docs/dokka/v0.1.0/scripts/pages.json
index f6790bc2..74c7e50a 100644
--- a/docs/dokka/v0.1.0/scripts/pages.json
+++ b/docs/dokka/v0.1.0/scripts/pages.json
@@ -1 +1 @@
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diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondExtras.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondExtras.kt
index e6dacf6c..ad408723 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondExtras.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondExtras.kt
@@ -11,5 +11,6 @@ package org.veupathdb.lib.cli.diamond
     "with extras enabled."
 )
 @Retention(AnnotationRetention.BINARY)
+@MustBeDocumented
 annotation class DiamondExtras
 
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondHidden.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondHidden.kt
index c83e656d..981c2006 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondHidden.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/DiamondHidden.kt
@@ -2,4 +2,5 @@ package org.veupathdb.lib.cli.diamond
 
 @RequiresOptIn("This feature is intentionally hidden in the DIAMOND tool.")
 @Retention(AnnotationRetention.BINARY)
+@MustBeDocumented
 annotation class DiamondHidden
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedGeneralOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedGeneralOptionContainerImpl.kt
index ba6687ea..a88e8fb6 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedGeneralOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedGeneralOptionContainerImpl.kt
@@ -4,12 +4,9 @@ import io.foxcapades.lib.cli.wrapper.flag.toggleFlag
 import io.foxcapades.lib.cli.wrapper.flag.ulongFlag
 import org.veupathdb.lib.cli.diamond.opts.AdvancedGeneralOptionContainer
 
-class AdvancedGeneralOptionContainerImpl : AdvancedGeneralOptionContainer {
+internal class AdvancedGeneralOptionContainerImpl : AdvancedGeneralOptionContainer {
   override var fileBufferSize by ulongFlag { default = 67108864u }
-
   override var noUnlink by toggleFlag()
-
   override var ignoreWarnings by toggleFlag()
-
   override var noParseSeqIDs by toggleFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedQueryOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedQueryOptionContainerImpl.kt
index 84fb0ae8..d61ddbd7 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedQueryOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AdvancedQueryOptionContainerImpl.kt
@@ -2,98 +2,53 @@ package org.veupathdb.lib.cli.diamond.opts.impl
 
 import io.foxcapades.lib.cli.wrapper.flag
 import io.foxcapades.lib.cli.wrapper.flag.*
-import io.foxcapades.lib.cli.wrapper.serial.values.ArgumentFormatter
 import org.veupathdb.lib.cli.diamond.opts.AdvancedQueryOptionContainer
 import org.veupathdb.lib.cli.diamond.opts.DNAExtensionAlgorithm
 import org.veupathdb.lib.cli.diamond.util.enumFormatter
-import java.nio.file.Path
 
-class AdvancedQueryOptionContainerImpl : AdvancedQueryOptionContainer {
+internal class AdvancedQueryOptionContainerImpl : AdvancedQueryOptionContainer {
   override var algo by stringFlag()
-
   override var minOrf by uintFlag()
-
   override var seedCut by doubleFlag()
-
   override var freqMasking by toggleFlag()
-
   override var freqStandardDeviation by doubleFlag()
-
   override var id2 by uintFlag()
-
   override var linsearch by toggleFlag()
-
   override var linStage1 by toggleFlag()
-
   override var xDrop by doubleFlag()
-
   override var gappedFilterEValue by doubleFlag()
-
   override var band by intFlag()
-
   override var shapeMask by flag<List<String>> { argument.shouldQuote = false }
-
   override var multiprocessing by toggleFlag()
-
   override var mpInit by toggleFlag()
-
   override var mpRecover by toggleFlag()
-
   override var mpQueryChunk by intFlag()
-
   override var cullingOverlap by doubleFlag()
-
   override var taxonK by ulongFlag()
-
   override var rangeCover by doubleFlag()
-
   override var xmlBlOrdFormat by toggleFlag()
-
   override var samQueryLen by toggleFlag()
-
   override var stopMatchScore by intFlag()
-
   override var targetIndexed by toggleFlag()
-
   override var unalignedTargets by pathFlag()
-
   override var cutBar by toggleFlag()
-
   override var checkMultiTarget by toggleFlag()
-
   override var rocFile by pathFlag()
-
   override var familyMap by pathFlag()
-
   override var familyMapQuery by pathFlag()
-
   override var queryParallelLimit by uintFlag { default = 3000000u }
-
   override var logEValueScale by doubleFlag()
-
   override var bootstrap by toggleFlag()
-
   override var heartbeat by toggleFlag()
-
   override var mpSelf by toggleFlag()
-
   override var zDrop by intFlag { default = 40 }
-
   override var repetitionCutoff by doubleFlag { default = 0.0002 }
-
   override var extension by flag<DNAExtensionAlgorithm> { argument.formatter = enumFormatter() }
-
   override var chainingOut by toggleFlag()
-
   override var alignLongReads by toggleFlag()
-
   override var chainPenGapScale by doubleFlag { default = 0.8 }
-
   override var chainPenSkipScale by doubleFlag { default = 0.0 }
-
   override var penalty by intFlag { default = -3 }
-
   override var reward by intFlag { default = 2 }
-
   override var queryOrSubjectCover by doubleFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringOptionContainerImpl.kt
index 30559210..410567fe 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringOptionContainerImpl.kt
@@ -7,12 +7,9 @@ import org.veupathdb.lib.cli.diamond.opts.ExtensionMode
 import org.veupathdb.lib.cli.diamond.opts.MotifMaskingAlgorithm
 import org.veupathdb.lib.cli.diamond.util.enumFormatter
 
-class AlignerClusteringOptionContainerImpl : AlignerClusteringOptionContainer {
+internal class AlignerClusteringOptionContainerImpl : AlignerClusteringOptionContainer {
   override var expectValue by doubleFlag { default = 0.001 }
-
   override var motifMasking by flag<MotifMaskingAlgorithm> { argument.formatter = enumFormatter() }
-
   override var approxIdentity by doubleFlag()
-
   override var extensionMode by flag<ExtensionMode> { argument.formatter = enumFormatter() }
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringRealignOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringRealignOptionContainerImpl.kt
index 620810f5..6712bfa8 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringRealignOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerClusteringRealignOptionContainerImpl.kt
@@ -5,7 +5,7 @@ import io.foxcapades.lib.cli.wrapper.flag.toggleFlag
 import org.veupathdb.lib.cli.diamond.opts.*
 import org.veupathdb.lib.cli.diamond.util.enumFormatter
 
-class AlignerClusteringRealignOptionContainerImpl : AlignerClusteringRealignOptionContainer {
+internal class AlignerClusteringRealignOptionContainerImpl : AlignerClusteringRealignOptionContainer {
   override var compBasedStats by flag<CompositionBasedStats> {
     default = CompositionBasedStats.Hauser
     argument.formatter = enumFormatter()
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerGeneralOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerGeneralOptionContainerImpl.kt
index 513af8a4..83f35340 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerGeneralOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerGeneralOptionContainerImpl.kt
@@ -8,7 +8,7 @@ import org.veupathdb.lib.cli.diamond.util.enumFlag
 import org.veupathdb.lib.cli.diamond.util.listFlag
 import java.nio.file.Path
 
-class AlignerGeneralOptionContainerImpl : AlignerGeneralOptionContainer {
+internal class AlignerGeneralOptionContainerImpl : AlignerGeneralOptionContainer {
   override var query by listFlag<Path>()
   override var strand by enumFlag<QueryStrand>()
   override var unalignedFile by pathFlag()
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerSensitivityOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerSensitivityOptionContainerImpl.kt
index bf5ea962..a4214110 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerSensitivityOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerSensitivityOptionContainerImpl.kt
@@ -5,7 +5,7 @@ import io.foxcapades.lib.cli.wrapper.util.MutableDefaultedProperty
 import org.veupathdb.lib.cli.diamond.opts.AlignerSensitivityOptionContainer
 import org.veupathdb.lib.cli.diamond.opts.Sensitivity
 
-class AlignerSensitivityOptionContainerImpl : AlignerSensitivityOptionContainer {
+internal class AlignerSensitivityOptionContainerImpl : AlignerSensitivityOptionContainer {
   override var sensitivity by MutableDefaultedProperty(Sensitivity.Default)
   override var shapes by uintFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerViewOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerViewOptionContainerImpl.kt
index e8b7ec2d..67155744 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerViewOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/AlignerViewOptionContainerImpl.kt
@@ -4,7 +4,7 @@ import io.foxcapades.lib.cli.wrapper.flag.doubleFlag
 import io.foxcapades.lib.cli.wrapper.flag.longFlag
 import org.veupathdb.lib.cli.diamond.opts.AlignerViewOptionContainer
 
-class AlignerViewOptionContainerImpl : AlignerViewOptionContainer {
+internal class AlignerViewOptionContainerImpl : AlignerViewOptionContainer {
   override var maxTargetSeqs by longFlag()
   override var top by doubleFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringGeneralOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringGeneralOptionContainerImpl.kt
index 0df5360f..d69e357d 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringGeneralOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringGeneralOptionContainerImpl.kt
@@ -4,7 +4,7 @@ import io.foxcapades.lib.cli.wrapper.flag
 import io.foxcapades.lib.cli.wrapper.flag.toggleFlag
 import org.veupathdb.lib.cli.diamond.opts.ClusteringGeneralOptionContainer
 
-class ClusteringGeneralOptionContainerImpl : ClusteringGeneralOptionContainer {
+internal class ClusteringGeneralOptionContainerImpl : ClusteringGeneralOptionContainer {
   override var clusterSteps by flag<List<String>> { argument.shouldQuote = false }
   override var kmerRanking by toggleFlag()
   override var roundCoverage by flag<List<String>> { argument.shouldQuote = false }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringInputOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringInputOptionContainerImpl.kt
index 7e332819..a13835a6 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringInputOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringInputOptionContainerImpl.kt
@@ -2,8 +2,7 @@ package org.veupathdb.lib.cli.diamond.opts.impl
 
 import io.foxcapades.lib.cli.wrapper.flag.pathFlag
 import org.veupathdb.lib.cli.diamond.opts.ClusteringInputOptionContainer
-import java.nio.file.Path
 
-class ClusteringInputOptionContainerImpl : ClusteringInputOptionContainer {
+internal class ClusteringInputOptionContainerImpl : ClusteringInputOptionContainer {
   override var clustersFile by pathFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringReassignOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringReassignOptionContainerImpl.kt
index 9f56cec8..69ee8be6 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringReassignOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ClusteringReassignOptionContainerImpl.kt
@@ -4,7 +4,7 @@ import io.foxcapades.lib.cli.wrapper.flag.doubleFlag
 import io.foxcapades.lib.cli.wrapper.flag.stringFlag
 import org.veupathdb.lib.cli.diamond.opts.ClusteringReassignOptionContainer
 
-class ClusteringReassignOptionContainerImpl : ClusteringReassignOptionContainer {
+internal class ClusteringReassignOptionContainerImpl : ClusteringReassignOptionContainer {
   override var memoryLimit by stringFlag()
   override var memberCover by doubleFlag { default = 80.0 }
   override var mutualCover by doubleFlag()
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralDBOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralDBOptionContainerImpl.kt
index 4f0abc21..988874a0 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralDBOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralDBOptionContainerImpl.kt
@@ -3,6 +3,6 @@ package org.veupathdb.lib.cli.diamond.opts.impl
 import io.foxcapades.lib.cli.wrapper.flag.pathFlag
 import org.veupathdb.lib.cli.diamond.opts.GeneralDBOptionContainer
 
-class GeneralDBOptionContainerImpl : GeneralDBOptionContainer {
+internal class GeneralDBOptionContainerImpl : GeneralDBOptionContainer {
   override var databaseFile by pathFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOptionContainerImpl.kt
index 5f487c6c..291cd2b2 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOptionContainerImpl.kt
@@ -5,7 +5,7 @@ import io.foxcapades.lib.cli.wrapper.flag.pathFlag
 import io.foxcapades.lib.cli.wrapper.flag.toggleFlag
 import org.veupathdb.lib.cli.diamond.opts.GeneralOptionContainer
 
-class GeneralOptionContainerImpl : GeneralOptionContainer {
+internal class GeneralOptionContainerImpl : GeneralOptionContainer {
   override var threads by intFlag()
   override var verbose by toggleFlag()
   override var log by toggleFlag()
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputHeaderOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputHeaderOptionContainerImpl.kt
index 3c567cf1..3e9d00b4 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputHeaderOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputHeaderOptionContainerImpl.kt
@@ -4,6 +4,6 @@ import io.foxcapades.lib.cli.wrapper.flag
 import org.veupathdb.lib.cli.diamond.opts.HeaderOption
 import org.veupathdb.lib.cli.diamond.opts.GeneralOutputHeaderOptionContainer
 
-class GeneralOutputHeaderOptionContainerImpl : GeneralOutputHeaderOptionContainer {
+internal class GeneralOutputHeaderOptionContainerImpl : GeneralOutputHeaderOptionContainer {
   override var header by flag<HeaderOption>() // TODO: custom implementation for optional arg var
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputOptionContainerImpl.kt
index bca1eadc..1e4b5566 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/GeneralOutputOptionContainerImpl.kt
@@ -3,6 +3,6 @@ package org.veupathdb.lib.cli.diamond.opts.impl
 import io.foxcapades.lib.cli.wrapper.flag.pathFlag
 import org.veupathdb.lib.cli.diamond.opts.GeneralOutputOptionContainer
 
-class GeneralOutputOptionContainerImpl : GeneralOutputOptionContainer {
+internal class GeneralOutputOptionContainerImpl : GeneralOutputOptionContainer {
   override var outputFile by pathFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/HiddenOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/HiddenOptionContainerImpl.kt
index aa11048f..72557ebe 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/HiddenOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/HiddenOptionContainerImpl.kt
@@ -5,7 +5,7 @@ import org.veupathdb.lib.cli.diamond.DiamondHidden
 import org.veupathdb.lib.cli.diamond.opts.*
 import org.veupathdb.lib.cli.diamond.util.enumFlag
 
-class HiddenOptionContainerImpl : HiddenOptionContainer {
+internal class HiddenOptionContainerImpl : HiddenOptionContainer {
   @DiamondHidden
   override var maximumSeedFrequency by doubleFlag()
 
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/OutputFormatOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/OutputFormatOptionContainerImpl.kt
index c12be087..8e34ba31 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/OutputFormatOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/OutputFormatOptionContainerImpl.kt
@@ -6,7 +6,7 @@ import io.foxcapades.lib.cli.wrapper.serial.values.ArgumentFormatter
 import org.veupathdb.lib.cli.diamond.opts.OutputFormatOptionContainer
 import org.veupathdb.lib.cli.diamond.opts.output_format.OutputFormatOptions
 
-class OutputFormatOptionContainerImpl : OutputFormatOptionContainer {
+internal class OutputFormatOptionContainerImpl : OutputFormatOptionContainer {
   override var outputFormat by flag<OutputFormatOptions> { argument.formatter = ArgumentFormatter.ofToString() }
   override var includeLineage by toggleFlag()
 }
diff --git a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ViewAlignOptionContainerImpl.kt b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ViewAlignOptionContainerImpl.kt
index bef900c9..e90cecf6 100644
--- a/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ViewAlignOptionContainerImpl.kt
+++ b/src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/ViewAlignOptionContainerImpl.kt
@@ -3,6 +3,6 @@ package org.veupathdb.lib.cli.diamond.opts.impl
 import io.foxcapades.lib.cli.wrapper.flag.pathFlag
 import org.veupathdb.lib.cli.diamond.opts.ViewAlignOptionContainer
 
-class ViewAlignOptionContainerImpl : ViewAlignOptionContainer {
+internal class ViewAlignOptionContainerImpl : ViewAlignOptionContainer {
   override var daa by pathFlag()
 }