PR comments

Author: ilyasoifer

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java

@@ -352,8 +352,8 @@ private AlleleLikelihoods<GATKRead, Allele> getAlleleLikelihoodMatrix(final Alle
                 .forEach(alleleHaplotypeMap.get(notAllele)::add);
 
         final AlleleLikelihoods<GATKRead, Allele> alleleLikelihoods = readLikelihoods.marginalize(alleleHaplotypeMap);
-        final SimpleInterval variantCallingRelevantFragmentOverlap = new SimpleInterval(allele).expandWithinContig(assemblyArgs.informativeReadOverlapMargin, sequenceDictionary);
-        alleleLikelihoods.retainEvidence(variantCallingRelevantFragmentOverlap::overlaps);
+        final SimpleInterval expandedVariantInterval = new SimpleInterval(allele).expandWithinContig(assemblyArgs.informativeReadOverlapMargin, sequenceDictionary);
+        alleleLikelihoods.retainEvidence(expandedVariantInterval::overlaps);
 
         logger.debug(() -> String.format("GALM: %s %d %d", allele, alleleHaplotypeMap.get(allele.altAllele()).size(), alleleHaplotypeMap.get(notAllele).size()));
         return alleleLikelihoods;

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringMutect.java

@@ -50,7 +50,7 @@ public AlleleFilteringMutect(M2ArgumentCollection _m2args,
      * This is very similar to what is done in the callMutations function in MutectEngine, but here the haplotypes that do
      * not support the allele are all haplotypes that do not contain the allele rather than only the haplotypes that support reference
      * etc.
-     * The log odds is calculated separately for the tumor and the normal samples and the smalles (the strongest) is returned
+     * The log odds is calculated separately for the tumor and the normal samples and the smallest (the strongest) is returned
      *
      * @param alleleLikelihoods
      * @param allele
@@ -64,6 +64,9 @@ int getAlleleLikelihoodVsInverse(final AlleleLikelihoods<GATKRead, Allele> allel
                 .filter(i -> !normalSamples.contains(alleleLikelihoods.getSample(i)))
                 .mapToObj(alleleLikelihoods::sampleMatrix)
                 .collect(Collectors.toList());
+        if (allMatrices.size()==0){
+            throw new GATKException.ShouldNeverReachHereException("No tumor samples found when calculating allele likelihood vs inverse");
+        }
         final AlleleList<Allele> alleleList = allMatrices.get(0);
         final LikelihoodMatrix<GATKRead, Allele> logAllMatrix = SomaticGenotypingEngine.combinedLikelihoodMatrix(allMatrices, alleleList);
         final double alleleLogOddsTumor = somaticAltLogOdds(logAllMatrix);