quick fix changes

broadinstitute · Sep 18, 2024 · fa1f0ee · fa1f0ee
1 parent 2104c0e
commit fa1f0ee
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java b/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
@@ -421,7 +421,7 @@ public int getDefaultCloudIndexPrefetchBufferSize() {
     public String getProgressMeterRecordLabel() { return ProgressMeter.DEFAULT_RECORD_LABEL; }
 
     /**
-     * @return null for no output filtering of variants to the variant writer.  Subclasses may override this to enforce other filtering schemes.
+     * @return default value does no filtering. Override to change how variants are filtered against the intervals for your tools.
      */
     public IntervalFilteringVcfWriter.Mode getVariantOutputFilteringMode(){
         return IntervalFilteringVcfWriter.Mode.ANYWHERE;

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/VariantWalkerBase.java b/src/main/java/org/broadinstitute/hellbender/engine/VariantWalkerBase.java
@@ -112,18 +112,12 @@ public SAMSequenceDictionary getBestAvailableSequenceDictionary() {
      */
     public abstract VCFHeader getHeaderForVariants();
 
-    /**
-     * @return Default interval filtering mode for variant output.  Subclasses may override this to set a different default.
-     */
-    public IntervalFilteringVcfWriter.Mode getDefaultVariantOutputFilterMode(){
-        return IntervalFilteringVcfWriter.Mode.ANYWHERE;
-    }
-
     @Override
     public IntervalFilteringVcfWriter.Mode getVariantOutputFilteringMode() {
         if (userOutputVariantIntervalFilteringMode != null) {
             return userOutputVariantIntervalFilteringMode;
         } else {
+            // Use whatever is the default provided by GATKTool
             return super.getVariantOutputFilteringMode();
         }
     }