Have Haplotype extend the Allele class.

This way, we don't need to create a new Allele for every read/Haplotype pair to be placed in the PerReadAlleleLikelihoodMap (very inefficient).  Also, now we can easily get the Haplotype associated with the best allele for a given read.

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

@@ -47,7 +47,6 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import com.google.java.contract.Ensures;
-import com.sun.corba.se.impl.logging.UtilSystemException;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
@@ -155,7 +154,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     protected StingSAMFileWriter bamWriter = null;
     private SAMFileHeader bamHeader = null;
     private long uniqueNameCounter = 1;
-    private final String readGroupId = "ArtificialHaplotype";
+    private final static String readGroupId = "ArtificialHaplotype";
 
     /**
      * The PairHMM implementation to use for genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.
@@ -338,20 +337,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
         genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS );
 
-        if ( bamWriter != null ) {
+        if ( bamWriter != null )
-            // prepare the bam header
+            setupBamWriter();
-            bamHeader = new SAMFileHeader();
-            bamHeader.setSequenceDictionary(getToolkit().getSAMFileHeader().getSequenceDictionary());
-            final List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>(1);
-            final SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupId);
-            rg.setSample("HC");
-            rg.setSequencingCenter("BI");
-            readGroups.add(rg);
-            bamHeader.setReadGroups(readGroups);
-            bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);
-            bamWriter.writeHeader(bamHeader);
-            bamWriter.setPresorted(true);
-        }
     }
 
     //---------------------------------------------------------------------------------------------------------------
@@ -461,8 +448,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES && activeAllelesToGenotype.isEmpty() ) { return 0; } // No alleles found in this region so nothing to do!
 
         finalizeActiveRegion( activeRegion ); // merge overlapping fragments, clip adapter and low qual tails
-        final Haplotype referenceHaplotype = new Haplotype(activeRegion.getActiveRegionReference(referenceReader)); // Create the reference haplotype which is the bases from the reference that make up the active region
+        final Haplotype referenceHaplotype = new Haplotype(activeRegion.getActiveRegionReference(referenceReader), true); // Create the reference haplotype which is the bases from the reference that make up the active region
-        referenceHaplotype.setIsReference(true);
         final byte[] fullReferenceWithPadding = activeRegion.getFullReference(referenceReader, REFERENCE_PADDING);
         //int PRUNE_FACTOR = Math.max(MIN_PRUNE_FACTOR, determinePruneFactorFromCoverage( activeRegion ));
         final ArrayList<Haplotype> haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, getPaddedLoc(activeRegion), MIN_PRUNE_FACTOR, activeAllelesToGenotype );
@@ -498,22 +484,19 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         }
 
         if ( bamWriter != null ) {
+            // sort the haplotypes in coordinate order and then write them to the bam
             Collections.sort( haplotypes, new Haplotype.HaplotypePositionComparator() );
             final GenomeLoc paddedRefLoc = getPaddedLoc(activeRegion);
-            for ( Haplotype haplotype : haplotypes ) {
+            for ( Haplotype haplotype : haplotypes )
-                // TODO -- clean up this code
+                writeHaplotype(haplotype, paddedRefLoc, bestHaplotypes.contains(haplotype));
-                final GATKSAMRecord record = new GATKSAMRecord(bamHeader);
+
-                record.setReadBases(haplotype.getBases());
+            // now, output the interesting reads for each sample
-                record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef());
+            for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) {
-                record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length));
+                for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) {
-                record.setCigar(haplotype.getCigar());
+                    final Allele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue());
-                record.setMappingQuality(bestHaplotypes.contains(haplotype) ? 60 : 0);
+                    if ( bestAllele != Allele.NO_CALL )
-                record.setReadName("HC" + uniqueNameCounter++);
+                        writeReadAgainstHaplotype(entry.getKey(), (Haplotype)bestAllele);
-                record.setReadUnmappedFlag(false);
+                }
-                record.setReferenceIndex(activeRegion.getReferenceLoc().getContigIndex());
-                record.setAttribute(SAMTag.RG.toString(), readGroupId);
-                record.setFlags(16);
-                bamWriter.addAlignment(record);
             }
         }
 
@@ -608,6 +591,46 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         }
 
         return returnMap;
+    }
+
+    private void setupBamWriter() {
+        // prepare the bam header
+        bamHeader = new SAMFileHeader();
+        bamHeader.setSequenceDictionary(getToolkit().getSAMFileHeader().getSequenceDictionary());
+        bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);
+
+        // include the original read groups plus a new artificial one for the haplotypes
+        final List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>(getToolkit().getSAMFileHeader().getReadGroups());
+        final SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupId);
+        rg.setSample("HC");
+        rg.setSequencingCenter("BI");
+        readGroups.add(rg);
+        bamHeader.setReadGroups(readGroups);
+
+        bamWriter.writeHeader(bamHeader);
+        bamWriter.setPresorted(true);
+    }
+
+    private void writeHaplotype(final Haplotype haplotype, final GenomeLoc paddedRefLoc, final boolean isAmongBestHaplotypes) {
+        final GATKSAMRecord record = new GATKSAMRecord(bamHeader);
+        record.setReadBases(haplotype.getBases());
+        record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef());
+        record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length));
+        record.setCigar(haplotype.getCigar());
+        record.setMappingQuality(isAmongBestHaplotypes ? 60 : 0);
+        record.setReadName("HC" + uniqueNameCounter++);
+        record.setReadUnmappedFlag(false);
+        record.setReferenceIndex(paddedRefLoc.getContigIndex());
+        record.setAttribute(SAMTag.RG.toString(), readGroupId);
+        record.setFlags(16);
+        bamWriter.addAlignment(record);
+    }
+
+    private void writeReadAgainstHaplotype(final GATKSAMRecord read, final Haplotype haplotype) {
+
+
+
+
     }
 
     /*

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

@@ -138,6 +138,7 @@ public class LikelihoodCalculationEngine {
                 readQuals[kkk] = ( readQuals[kkk] > (byte) read.getMappingQuality() ? (byte) read.getMappingQuality() : readQuals[kkk] ); // cap base quality by mapping quality
                 //readQuals[kkk] = ( readQuals[kkk] > readInsQuals[kkk] ? readInsQuals[kkk] : readQuals[kkk] ); // cap base quality by base insertion quality, needs to be evaluated
                 //readQuals[kkk] = ( readQuals[kkk] > readDelQuals[kkk] ? readDelQuals[kkk] : readQuals[kkk] ); // cap base quality by base deletion quality, needs to be evaluated
+                // TODO -- why is Q18 hard-coded here???
                 readQuals[kkk] = ( readQuals[kkk] < (byte) 18 ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
             }
 
@@ -151,7 +152,7 @@ public class LikelihoodCalculationEngine {
                 final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) );
                 previousHaplotypeSeen = haplotype;
 
-                perReadAlleleLikelihoodMap.add(read, Allele.create(haplotype.getBases()),
+                perReadAlleleLikelihoodMap.add(read, haplotype,
                         pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype.getBases(), read.getReadBases(),
                                 readQuals, readInsQuals, readDelQuals, overallGCP, haplotypeStart, jjj == 0));
             }

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

@@ -37,57 +37,69 @@ import org.broadinstitute.variant.variantcontext.VariantContext;
 import java.io.Serializable;
 import java.util.*;
 
-public class Haplotype {
+public class Haplotype  extends Allele {
-    protected final byte[] bases;
     protected final double[] quals;
     private GenomeLoc genomeLocation = null;
     private HashMap<Integer, VariantContext> eventMap = null;
-    private boolean isRef = false;
     private Cigar cigar;
     private int alignmentStartHapwrtRef;
     public int leftBreakPoint = 0;
     public int rightBreakPoint = 0;
     private Event artificialEvent = null;
 
+    /**
+     * Main constructor
+     *
+     * @param bases bases
+     * @param quals quals
+     * @param isRef is reference allele?
+     */
+    public Haplotype( final byte[] bases, final double[] quals, final boolean isRef ) {
+        super(bases.clone(), isRef);
+        this.quals = quals.clone();
+    }
+
     /**
      * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual
      *
      * @param bases bases
      * @param qual  qual
      */
-    public Haplotype( final byte[] bases, final int qual ) {
+    public Haplotype( final byte[] bases, final int qual, final boolean isRef ) {
-        this.bases = bases.clone();
+        super(bases.clone(), isRef);
         quals = new double[bases.length];
         Arrays.fill(quals, (double)qual);
     }
 
+    public Haplotype( final byte[] bases, final int qual ) {
+        this(bases, qual, false);
+    }
+
+    public Haplotype( final byte[] bases, final boolean isRef ) {
+        this(bases, 0, isRef);
+    }
+
     public Haplotype( final byte[] bases, final double[] quals ) {
-        this.bases = bases.clone();
+        this(bases, quals, false);
-        this.quals = quals.clone();
     }
 
     public Haplotype( final byte[] bases ) {
-        this(bases, 0);
+        this(bases, 0, false);
     }
 
     protected Haplotype( final byte[] bases, final Event artificialEvent ) {
-        this(bases, 0);
+        this(bases, 0, false);
         this.artificialEvent = artificialEvent;
     }
 
     public Haplotype( final byte[] bases, final GenomeLoc loc ) {
-        this(bases);
+        this(bases, 0, false);
         this.genomeLocation = loc;
     }
 
     @Override
     public boolean equals( Object h ) {
-        return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases);
+        return h instanceof Haplotype && super.equals(h);
-    }
-    
-    @Override
-    public int hashCode() {
-        return Arrays.hashCode(bases);
     }
     
     public HashMap<Integer, VariantContext> getEventMap() {
@@ -98,17 +110,9 @@ public class Haplotype {
         this.eventMap = eventMap;
     }
 
-    public boolean isReference() {
-        return isRef;
-    }
-
-    public void setIsReference( boolean isRef ) {
-        this.isRef = isRef;
-    }
-
     public double getQualitySum() {
         double s = 0;
-        for (int k=0; k < bases.length; k++) {
+        for (int k=0; k < quals.length; k++) {
             s += quals[k];
         }
         return s;
@@ -116,14 +120,14 @@ public class Haplotype {
 
     @Override
     public String toString() {
-        return new String(bases);
+        return getDisplayString();
     }
 
     public double[] getQuals() {
         return quals.clone();
     }
     public byte[] getBases() {
-        return bases.clone();
+        return super.getBases().clone();
     }
 
     public long getStartPosition() {
@@ -178,13 +182,13 @@ public class Haplotype {
     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() >= bases.length ) { // desired change falls inside deletion so don't bother creating a new haplotype
+        if( haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= getBases().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(bases, 0, haplotypeInsertLocation)); // bases before the variant
+        newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(getBases(), 0, haplotypeInsertLocation)); // bases before the variant
         newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant
-        newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(bases, haplotypeInsertLocation + refAllele.length(), bases.length)); // bases after the variant
+        newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(getBases(), haplotypeInsertLocation + refAllele.length(), getBases().length)); // bases after the variant
         return new Haplotype(newHaplotypeBases, new Event(refAllele, altAllele, genomicInsertLocation));
     }
 

public/java/src/org/broadinstitute/variant/variantcontext/Allele.java

@@ -111,7 +111,7 @@ public class Allele implements Comparable<Allele> {
     /** A generic static NO_CALL allele for use */
 
     // no public way to create an allele
-    private Allele(byte[] bases, boolean isRef) {
+    protected Allele(byte[] bases, boolean isRef) {
         // null alleles are no longer allowed
         if ( wouldBeNullAllele(bases) ) {
             throw new IllegalArgumentException("Null alleles are not supported");
@@ -140,7 +140,7 @@ public class Allele implements Comparable<Allele> {
             throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'");
     }
 
-    private Allele(String bases, boolean isRef) {
+    protected Allele(String bases, boolean isRef) {
         this(bases.getBytes(), isRef);
     }