fixing a logic error for an underutilized codepath for event filtering

broadinstitute · Jan 30, 2023 · 0ae8da5 · 0ae8da5
1 parent 52b3037
commit 0ae8da5
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/...institute/hellbender/tools/walkers/haplotypecaller/PileupDetectionArgumentCollection.java b/...institute/hellbender/tools/walkers/haplotypecaller/PileupDetectionArgumentCollection.java
@@ -147,7 +147,7 @@ public final class PileupDetectionArgumentCollection {
      */
     @Advanced
     @Hidden
-    @Argument(fullName= PILEUP_DETECTION_FILTER_ASSEMBLY_HAPS_THRESHOLD, doc = "If enabled (set to non-zero), will apply the \"badness\" filter to compatable assembled haplotypes.", optional = true)
+    @Argument(fullName= PILEUP_DETECTION_FILTER_ASSEMBLY_HAPS_THRESHOLD, doc = "If enabled (set to non-zero), will apply the \"badness\" filter to compatible assembled haplotypes.", optional = true)
     public double assemblyBadReadThreshold = 0.4;
     @Hidden
     @Argument(fullName= PILEUP_DETECTION_EDIT_DISTANCE_BADNESS_FOR_ASSEMBLY_LONG_NAME, doc = "Pileup Detection: Reject alt reads with greater than this fraction of mismatching bases from the reference (proxied using the NM tag). (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupBasedAlleles.java b/src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupBasedAlleles.java
@@ -189,7 +189,7 @@ public static boolean shouldFilterAssemblyVariant(final PileupDetectionArgumentC
         validatePileupVariant(pileupVariant);
         final int pileupSupport = pileupVariant.getAttributeAsInt(PILEUP_ALLELE_SUPPORTING_READS, 0);
         final int assemblyBadReads = pileupVariant.getAttributeAsInt(PILEUP_ALLELE_ASSEMBLY_BAD_READS_TAG, 0);
-        return ((args.assemblyBadReadThreshold <= 0.0) && (double) assemblyBadReads / (double) pileupSupport >= args.assemblyBadReadThreshold);
+        return ((args.assemblyBadReadThreshold > 0.0) && (double) assemblyBadReads / (double) pileupSupport >= args.assemblyBadReadThreshold);
     }
 
     private static void validatePileupVariant(final VariantContext pileupVariant) {