Innocuous housekeeping changes in the partially determined haplotypes…

… code (#8361)
broadinstitute · Jun 25, 2023 · a86d8a3 · a86d8a3
1 parent bb22de4
commit a86d8a3
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Showing 11 changed files with 489 additions and 467 deletions.
diff --git a/...a/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleLikelihoodWriter.java b/...a/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleLikelihoodWriter.java
@@ -52,9 +52,9 @@ public void writeAlleleLikelihoods(final AlleleLikelihoods<GATKRead, Haplotype>
 
         final Haplotype first_hap = haplotypes.get(0);
         try {
-            if (outputInterval == null || outputInterval.contains(first_hap.getLocation())) {
-                output.write(String.format("> Location %s:%d-%d\n", first_hap.getLocation().getContig(),
-                        first_hap.getStartPosition(), first_hap.getStopPosition()));
+            if (outputInterval == null || outputInterval.contains(first_hap)) {
+                output.write(String.format("> Location %s:%d-%d\n", first_hap.getContig(),
+                        first_hap.getStart(), first_hap.getEnd()));
                 output.write(">> Haplotypes\n");
                 for (int i = 0; i < haplotypes.size(); i++) {
                     output.write(String.format("%04d\t%s\n", i, haplotypes.get(i).toString()));

diff --git a/...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
@@ -706,16 +706,10 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
                 System.out.println("CallingSpan: " + region.getSpan());
             }
             assemblyResult = PartiallyDeterminedHaplotypeComputationEngine.generatePDHaplotypes(assemblyResult,
-                    region.getSpan(),
-                    assemblyResult.getReferenceHaplotype(),
-                    assemblyVariants,
                     badPileupEvents,
                     goodPileupEvents,
-                    hcArgs.pileupDetectionArgs.snpAdjacentToAssemblyIndel,
                     aligner,
-                    hcArgs.getHaplotypeToReferenceSWParameters(),
-                    hcArgs.pileupDetectionArgs.determinePDHaps,
-                    hcArgs.pileupDetectionArgs.debugPileupStdout);
+                    hcArgs);
         }
 
         // Legacy Pileupcaller code. Supplement the assembly haps with artifical haps constructed from the discovered pileupcaller
@@ -773,13 +767,13 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
         if (HaplotypeCallerGenotypingDebugger.isEnabled()) {
             HaplotypeCallerGenotypingDebugger.println("\nUnclipped Haplotypes("+haplotypes.size()+"):");
             for (Haplotype haplotype : untrimmedAssemblyResult.getHaplotypeList()) {
-                HaplotypeCallerGenotypingDebugger.println("["+haplotype.getStartPosition()+"-"+haplotype.getStopPosition()+"] k="+haplotype.getKmerSize()+" len: "+haplotype.length()+" "+haplotype.getCigar()+(haplotype.isReference()?"ref":""));
+                HaplotypeCallerGenotypingDebugger.println("["+haplotype.getStart()+"-"+haplotype.getEnd()+"] k="+haplotype.getKmerSize()+" len: "+haplotype.length()+" "+haplotype.getCigar()+(haplotype.isReference()?"ref":""));
                 HaplotypeCallerGenotypingDebugger.println(haplotype.toString());
             }
 
             HaplotypeCallerGenotypingDebugger.println("\nClipped Haplotyes("+haplotypes.size()+"):");
             for (Haplotype haplotype : haplotypes) {
-                HaplotypeCallerGenotypingDebugger.println("["+haplotype.getStartPosition()+"-"+haplotype.getStopPosition()+"] k="+haplotype.getKmerSize()+" len: "+haplotype.length()+" "+haplotype.getCigar()+(haplotype.isReference()?"ref":""));
+                HaplotypeCallerGenotypingDebugger.println("["+haplotype.getStart()+"-"+haplotype.getEnd()+"] k="+haplotype.getKmerSize()+" len: "+haplotype.length()+" "+haplotype.getCigar()+(haplotype.isReference()?"ref":""));
                 HaplotypeCallerGenotypingDebugger.println(haplotype.toString());
             }
             HaplotypeCallerGenotypingDebugger.println("");

diff --git a/...llbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java b/...llbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java
diff --git a/...ain/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ramps/RampUtils.java b/...ain/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ramps/RampUtils.java
@@ -62,11 +62,11 @@ public int compare(final Haplotype o1, final Haplotype o2) {
             int         delta = (o1.isReference() ? 1 : 0) - (o2.isReference() ? 1 : 0);
 
             if ( delta == 0 ) {
-                delta = o1.getLocation().getContig().compareTo(o2.getLocation().getContig());
+                delta = o1.getContig().compareTo(o2.getContig());
                 if ( delta == 0 ) {
-                    delta = o1.getLocation().getStart() - o2.getLocation().getStart();
+                    delta = o1.getStart() - o2.getStart();
                     if ( delta == 0 ) {
-                        delta = o1.getLocation().getEnd() - o2.getLocation().getEnd();
+                        delta = o1.getEnd() - o2.getEnd();
                         if ( delta == 0 ) {
                             double      ddelta = o1.getScore() - o2.getScore();
                             if ( ddelta < 0 )