fix vcf site walker failing on hom-ref calls when walking alleles

ssadedin · Jun 18, 2024 · 79db1db · 79db1db
1 parent 3bd3284
commit 79db1db
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/src/main/groovy/gngs/VCFSiteWalker.groovy b/src/main/groovy/gngs/VCFSiteWalker.groovy
@@ -161,7 +161,10 @@ class VCFSiteWalker {
     @CompileStatic
     private void processByAllele(List<VariantContext> variants, @ClosureParams(value=FromString, options='java.util.List<htsjdk.variant.variantcontext.VariantContext>') Closure callback) {
         Map<String, List<VariantContext>> alleles = variants.groupBy { VariantContext ctx ->
-            ctx.getReference().baseString + '/' + ctx.getAlternateAllele(0).baseString
+            if(ctx.isVariant())
+                ctx.getReference().baseString + '/' + ctx.getAlternateAllele(0).baseString
+            else
+                ctx.getReference().baseString + '/' + ctx.getReference().baseString
         }
 
         alleles.each { String bases, List<VariantContext> alleleVariants ->