a few very minor comment tweaks

broadinstitute · Jan 30, 2023 · a70603e · a70603e
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commit a70603e
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diff --git a/...org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java b/...org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java
@@ -444,6 +444,9 @@ public static AssemblyResultSet applyPileupEventsAsForcedAlleles(final AssemblyR
                                                                       final AssemblyResultSet assemblyResultSet, final List<VariantContext> pileupAllelesFoundShouldFilter,
                                                                       final List<VariantContext> pileupAllelesPassingFilters, final boolean debug) {
         List<Haplotype> haplotypesWithFilterAlleles = new ArrayList<>();
+        // IF we find pileup alleles that we want to filter... AND we are not generating the partially determined haplotypes,
+        // we resort to a messy approach where we filter alleles by throwing away every haplotype supporting an allele. This is
+        // very dangerous since this could easily destroy phased variants with the haplotype.
         if (!pileupAllelesFoundShouldFilter.isEmpty() && !argumentCollection.pileupDetectionArgs.generatePDHaplotypes) {
             // TODO this is a bad algorithm for bad people
             for(VariantContext delVariant : pileupAllelesFoundShouldFilter) {

diff --git a/...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
@@ -671,19 +671,22 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
                 .filter(v -> PileupBasedAlleles.passesFilters(hcArgs.pileupDetectionArgs, v))
                 .collect(Collectors.toList());
 
+        // Regenerate the list of AllVariationEvents, filtering out assembled variants that must be filtered according to the pileupcaller code.
         final SortedSet<VariantContext> allVariationEvents = new TreeSet<>(
                 AssemblyResultSet.HAPLOTYPE_VARIANT_CONTEXT_COMPARATOR);
         allVariationEvents.addAll(untrimmedAssemblyResult.getVariationEvents(hcArgs.maxMnpDistance).stream()
                 .filter(outerVC -> { return pileupAllelesFoundShouldFilter.stream().noneMatch(filterAllle -> filterAllle.getStart() == outerVC.getStart()
                         && filterAllle.getReference().equals(outerVC.getReference())
                         && filterAllle.getAlternateAllele(0).equals(outerVC.getAlternateAllele(0)));
                 }).collect(Collectors.toList()));
+        // Add any new pileupcaller alleles to the variation events
         for (final VariantContext pileupAllele : pileupAllelesPassingFilters) {
             //these are events from single haplotypes, so we can do a simple comparison without trimming
             if (allVariationEvents.stream().noneMatch(vc -> vc.getStart() == pileupAllele.getStart() && vc.getAlternateAllele(0).basesMatch(pileupAllele.getAlternateAllele(0)))) {
                 allVariationEvents.add(pileupAllele);
             }
         }
+        // Add given alleles to the variation events
         for (final VariantContext given : givenAlleles) {
             //these are events from single haplotypes, so we can do a simple comparison without trimming
             if (allVariationEvents.stream().noneMatch(vc -> vc.getStart() == given.getStart() && vc.getAlternateAllele(0).basesMatch(given.getAlternateAllele(0)))) {