Merge pull request #51 from broadinstitute/eb_optimize_hc_haplotype_comparisons

Haplotype/Allele based optimizations for the HaplotypeCaller that knock ...

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java

@@ -368,7 +368,7 @@ public class GenotypingEngine {
                 for( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> readEntry : haplotypeReadMapEntry.getValue().getLikelihoodReadMap().entrySet() ) { // for each read
                     double maxLikelihood = Double.NEGATIVE_INFINITY;
                     for( final Map.Entry<Allele,Double> alleleDoubleEntry : readEntry.getValue().entrySet() ) { // for each input allele
-                        if( mappedHaplotypes.contains( new Haplotype(alleleDoubleEntry.getKey().getBases())) ) { // exact match of haplotype base string
+                        if( mappedHaplotypes.contains( new Haplotype(alleleDoubleEntry.getKey())) ) { // exact match of haplotype base string
                             maxLikelihood = Math.max( maxLikelihood, alleleDoubleEntry.getValue() );
                         }
                     }
@@ -442,7 +442,7 @@ public class GenotypingEngine {
                         }
                         // count up the co-occurrences of the events for the R^2 calculation
                         for( final String sample : samples ) {
-                            final double haplotypeLikelihood = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods( Collections.singleton(sample), haplotypeReadMap, Collections.singletonList(Allele.create(h.getBases())) )[0][0];
+                            final double haplotypeLikelihood = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods( Collections.singleton(sample), haplotypeReadMap, Collections.singletonList(Allele.create(h, true)) )[0][0];
                             if( thisHapVC == null ) {
                                 if( nextHapVC == null ) { x11 = MathUtils.approximateLog10SumLog10(x11, haplotypeLikelihood); }
                                 else { x12 = MathUtils.approximateLog10SumLog10(x12, haplotypeLikelihood); }

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java

@@ -125,7 +125,7 @@ public class LikelihoodCalculationEngine {
         final int numHaplotypes = haplotypes.size();
         final Map<Haplotype, Allele> alleleVersions = new HashMap<Haplotype, Allele>(numHaplotypes);
         for ( final Haplotype haplotype : haplotypes ) {
-            alleleVersions.put(haplotype, Allele.create(haplotype.getBases()));
+            alleleVersions.put(haplotype, Allele.create(haplotype, true));
         }
 
         final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
@@ -232,7 +232,7 @@ public class LikelihoodCalculationEngine {
         final List<Integer> bestHaplotypesIndexList = new ArrayList<Integer>();
         bestHaplotypesIndexList.add( findReferenceIndex(haplotypes) ); // always start with the reference haplotype
         final List<Allele> haplotypesAsAlleles = new ArrayList<Allele>();
-        for( final Haplotype h : haplotypes ) { haplotypesAsAlleles.add(Allele.create(h.getBases())); }
+        for( final Haplotype h : haplotypes ) { haplotypesAsAlleles.add(Allele.create(h, true)); }
 
         final double[][] haplotypeLikelihoodMatrix = computeDiploidHaplotypeLikelihoods( sampleKeySet, stratifiedReadMap, haplotypesAsAlleles ); // all samples pooled together
 

public/java/src/org/broadinstitute/sting/utils/Haplotype.java

@@ -61,6 +61,15 @@ public class Haplotype extends Allele {
         this(bases, false);
     }
 
+    /**
+     * Copy constructor.  Note the ref state of the provided allele is ignored!
+     *
+     * @param allele allele to copy
+     */
+    public Haplotype( final Allele allele ) {
+        super(allele, true);
+    }
+
     protected Haplotype( final byte[] bases, final Event artificialEvent ) {
         this(bases, false);
         this.artificialEvent = artificialEvent;
@@ -94,10 +103,6 @@ public class Haplotype extends Allele {
         return getDisplayString();
     }
 
-    public byte[] getBases() {
-        return super.getBases().clone();
-    }
-
     public long getStartPosition() {
         return genomeLocation.getStart();
     }
@@ -150,13 +155,15 @@ public class Haplotype extends Allele {
     public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, final int refInsertLocation, final int genomicInsertLocation ) {
         // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates
         final int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true);
-        if( haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= getBases().length ) { // desired change falls inside deletion so don't bother creating a new haplotype
+        final byte[] myBases = this.getBases();
+        if( haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= myBases.length ) { // desired change falls inside deletion so don't bother creating a new haplotype
             return null;
         }
+
         byte[] newHaplotypeBases = new byte[]{};
-        newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(getBases(), 0, haplotypeInsertLocation)); // bases before the variant
+        newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(myBases, 0, haplotypeInsertLocation)); // bases before the variant
         newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant
-        newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(getBases(), haplotypeInsertLocation + refAllele.length(), getBases().length)); // bases after the variant
+        newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(myBases, haplotypeInsertLocation + refAllele.length(), myBases.length)); // bases after the variant
         return new Haplotype(newHaplotypeBases, new Event(refAllele, altAllele, genomicInsertLocation));
     }
 
@@ -199,7 +206,7 @@ public class Haplotype extends Allele {
         if (refAllele == null)
             throw new ReviewedStingException("BUG: no ref alleles in input to makeHaplotypeListfrom Alleles at loc: "+ startPos);
 
-        byte[] refBases = ref.getBases();
+        final byte[] refBases = ref.getBases();
 
         final int startIdxInReference = 1 + startPos - numPrefBases - ref.getWindow().getStart();
         final String basesBeforeVariant = new String(Arrays.copyOfRange(refBases, startIdxInReference, startIdxInReference + numPrefBases));

settings/repository/org.broadinstitute/variant-1.85.1357.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.84.1338" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.85.1357" status="integration" />
 </ivy-module>