Warn on unrecognized options (fixes #25) (#118)

disq-bio · Sep 9, 2019 · 8dd2362 · 8dd2362
1 parent 8cfd528
commit 8dd2362
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diff --git a/src/main/java/org/disq_bio/disq/HtsjdkReadsRddStorage.java b/src/main/java/org/disq_bio/disq/HtsjdkReadsRddStorage.java
@@ -40,10 +40,14 @@
 import org.disq_bio.disq.impl.file.NioFileSystemWrapper;
 import org.disq_bio.disq.impl.formats.sam.AbstractSamSource;
 import org.disq_bio.disq.impl.formats.sam.SamFormat;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /** The entry point for reading or writing a {@link HtsjdkReadsRdd}. */
 public class HtsjdkReadsRddStorage {
 
+  private static final Logger logger = LoggerFactory.getLogger(HtsjdkReadsRddStorage.class);
+
   private JavaSparkContext sparkContext;
   private int splitSize;
   private ValidationStringency validationStringency = ValidationStringency.DEFAULT_STRINGENCY;
@@ -199,6 +203,8 @@ public void write(HtsjdkReadsRdd htsjdkReadsRdd, String path, WriteOption... wri
         indexesToEnable.add(CraiWriteOption.getIndexExtension());
       } else if (writeOption instanceof SbiWriteOption && writeOption == SbiWriteOption.ENABLE) {
         indexesToEnable.add(SbiWriteOption.getIndexExtension());
+      } else {
+        logger.warn("Unrecognized write option: {}", writeOption);
       }
     }
 

diff --git a/src/main/java/org/disq_bio/disq/HtsjdkVariantsRddStorage.java b/src/main/java/org/disq_bio/disq/HtsjdkVariantsRddStorage.java
@@ -35,10 +35,14 @@
 import org.apache.spark.api.java.JavaSparkContext;
 import org.disq_bio.disq.impl.formats.vcf.VcfFormat;
 import org.disq_bio.disq.impl.formats.vcf.VcfSource;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /** The entry point for reading or writing a {@link HtsjdkVariantsRdd}. */
 public class HtsjdkVariantsRddStorage {
 
+  private static final Logger logger = LoggerFactory.getLogger(HtsjdkVariantsRddStorage.class);
+
   private JavaSparkContext sparkContext;
   private int splitSize;
 
@@ -122,6 +126,8 @@ public void write(HtsjdkVariantsRdd htsjdkVariantsRdd, String path, WriteOption.
       } else if (writeOption instanceof TabixIndexWriteOption
           && writeOption == TabixIndexWriteOption.ENABLE) {
         indexesToEnable.add(TabixIndexWriteOption.getIndexExtension());
+      } else {
+        logger.warn("Unrecognized write option: {}", writeOption);
       }
     }