Threshold updated

broadinstitute · Jun 6, 2024 · b852ec7 · b852ec7
1 parent 3e94754
commit b852ec7
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Showing 3 changed files with 5 additions and 25 deletions.
diff --git a/...ain/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java b/...ain/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java
@@ -43,18 +43,19 @@
  */
 
 public abstract class AlleleFiltering {
-
     final protected static Logger logger = LogManager.getLogger(AlleleFiltering.class);
     final protected AssemblyBasedCallerArgumentCollection assemblyArgs;
     final private OutputStreamWriter assemblyDebugOutStream;
     final private SAMSequenceDictionary sequenceDictionary;
+
     AlleleFiltering(final AssemblyBasedCallerArgumentCollection assemblyArgs,
                     final OutputStreamWriter assemblyDebugOutStream,
                     final SAMFileHeader header){
         this.assemblyArgs = assemblyArgs;
         this.assemblyDebugOutStream = assemblyDebugOutStream;
         this.sequenceDictionary = header.getSequenceDictionary();
     }
+    protected abstract double getStringentQuality();
 
     /**
      * Finds alleles that are likely not contributing much to explaining the data and remove the haplotypes
@@ -204,8 +205,7 @@ private AlleleLikelihoods<GATKRead, Haplotype> subsetHaplotypesByAlleles(final A
                 // the very weak quality is hardcoded
                 final List<Event> filteringCandidatesStringent = identifyBadAlleles(collectedRPLs,
                         collectedSORs,
-                        activeAlleles,
-                        1,
+                        activeAlleles, getStringentQuality(),
                         Integer.MAX_VALUE);
 
 

diff --git a/...n/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java b/...n/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
@@ -35,6 +35,7 @@ public AlleleFilteringHC(HaplotypeCallerArgumentCollection _hcargs, OutputStream
          afCalc = AlleleFrequencyCalculator.makeCalculator(config);
     }
 
+    protected double getStringentQuality() { return 1; }
     /**
      * Calculate genotype likelihood of requirement of an allele. Specifically, calculates the likelihood
      * of the data given that allele versus the likelihood of the data when all haplotypes containing the allele are removed

diff --git a/...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringMutect.java b/...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringMutect.java
@@ -42,28 +42,7 @@ public AlleleFilteringMutect(M2ArgumentCollection _m2args,
         normalSamples = _normalSamples;
     }
 
-    private AlleleLikelihoods<GATKRead, Allele> getAlleleLikelihoodMatrix(final AlleleLikelihoods<GATKRead, Haplotype> readLikelihoods,
-                                                                          final Event allele,
-                                                                          final Map<Haplotype, Collection<Event>> haplotypeAlleleMap,
-                                                                          final Set<Haplotype> enabledHaplotypes
-    ){
-
-        final Map<Allele,List<Haplotype>> alleleHaplotypeMap = new CollectionUtil.DefaultingMap<>((k) -> new ArrayList<>(), true);
-
-
-        final Allele notAllele= InverseAllele.of(allele.altAllele(), true);
-        readLikelihoods.alleles().stream().filter(enabledHaplotypes::contains)
-                .filter(h->haplotypeAlleleMap.get(h).contains(allele))
-                .forEach(alleleHaplotypeMap.get(allele.altAllele())::add);
-        readLikelihoods.alleles().stream().filter(enabledHaplotypes::contains)
-                .filter(h -> !haplotypeAlleleMap.get(h).contains(allele))
-                .forEach(alleleHaplotypeMap.get(notAllele)::add);
-
-        final AlleleLikelihoods<GATKRead, Allele> alleleLikelihoods = readLikelihoods.marginalize(alleleHaplotypeMap);
-
-        logger.debug(() -> String.format("GALM: %s %d %d", allele, alleleHaplotypeMap.get(allele.altAllele()).size(), alleleHaplotypeMap.get(notAllele).size()));
-        return alleleLikelihoods;
-    }
+    protected double getStringentQuality() { return -50; }
 
     /**
      * Calculate calculate genotype likelihood of requirement of an allele. Specifically, calculates the likelihood