First step in refactoring UG way of storing indel likelihoods - main motive is that rank sum annotations require per-read quality or likelihood information, and even the question "what allele of a variant is present in a read" which is trivial for SNPs may not be that straightforward for indels.

This step just changes storage of likelihoods so now we have, instead of an internal matrix, a class member which stores, as a hash table, a mapping from pileup element to an (allele, likelihood) pair. There's no functional change aside from internal data storage.
As a bonus, we get for free a 2-3x improvement in speed in calling because redundant likelihood computations are removed.
Next step will hook this up to, and redefine annotation engine interaction with UG for indel case.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5809 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java

@@ -34,10 +34,12 @@ import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -57,9 +59,13 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
     private boolean DEBUG = false;
 
     private PairHMMIndelErrorModel pairModel;
-// gdebug removeme
+
-// todo -cleanup
+    private HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap;
-private HaplotypeIndelErrorModel model;
+    private LinkedHashMap<Allele,Haplotype> haplotypeMap;
+
+    // gdebug removeme
+    // todo -cleanup
+    private HaplotypeIndelErrorModel model;
     private boolean useOldWrongHorribleHackedUpLikelihoodModel = false;
 //
     private GenomeLoc lastSiteVisited;
@@ -84,6 +90,7 @@ private HaplotypeIndelErrorModel model;
             model = new HaplotypeIndelErrorModel(3, INSERTION_START_PROBABILITY,
                     INSERTION_END_PROBABILITY,ALPHA_DELETION_PROBABILITY,UAC.INDEL_HAPLOTYPE_SIZE, false, UAC.OUTPUT_DEBUG_INDEL_INFO);
         }
+
         pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY,UAC.INDEL_GAP_CONTINUATION_PENALTY,
                     UAC.OUTPUT_DEBUG_INDEL_INFO, UAC.DO_CONTEXT_DEPENDENT_PENALTIES, UAC.dovit, UAC.GET_GAP_PENALTIES_FROM_DATA, UAC.INDEL_RECAL_FILE);
         alleleList = new ArrayList<Allele>();
@@ -91,6 +98,10 @@ private HaplotypeIndelErrorModel model;
         minIndelCountForGenotyping = UAC.MIN_INDEL_COUNT_FOR_GENOTYPING;
         HAPLOTYPE_SIZE = UAC.INDEL_HAPLOTYPE_SIZE;
         DEBUG = UAC.OUTPUT_DEBUG_INDEL_INFO;
+
+        indelLikelihoodMap = new HashMap<PileupElement,LinkedHashMap<Allele,Double>>();
+        haplotypeMap = new LinkedHashMap<Allele,Haplotype>();
+
     }
 
 
@@ -294,7 +305,8 @@ private HaplotypeIndelErrorModel model;
             // starting a new site: clear allele list
             alleleList.clear();
             lastSiteVisited = ref.getLocus().clone();
-
+            indelLikelihoodMap.clear();
+            haplotypeMap.clear();
 
             if (getAlleleListFromVCF) {
 
@@ -341,7 +353,7 @@ private HaplotypeIndelErrorModel model;
         int eventLength = altAllele.getBaseString().length() - refAllele.getBaseString().length();
         // assume only one alt allele for now
 
-        List<Haplotype> haplotypesInVC;
+        //List<Haplotype> haplotypesInVC;
 
         int hsize = (int)ref.getWindow().size()-Math.abs(eventLength)-1;
         int numPrefBases= ref.getLocus().getStart()-ref.getWindow().getStart()+1;
@@ -354,7 +366,7 @@ private HaplotypeIndelErrorModel model;
             System.out.format("hsize: %d eventLength: %d refSize: %d, locStart: %d numpr: %d\n",hsize,eventLength,
                     (int)ref.getWindow().size(), loc.getStart(), numPrefBases);
 
-        haplotypesInVC = Haplotype.makeHaplotypeListFromAlleles( alleleList, loc.getStart(),
+        haplotypeMap = Haplotype.makeHaplotypeListFromAlleles( alleleList, loc.getStart(),
             ref, hsize, numPrefBases);
 
         // For each sample, get genotype likelihoods based on pileup
@@ -362,9 +374,6 @@ private HaplotypeIndelErrorModel model;
         // initialize the GenotypeLikelihoods
         GLs.clear();
 
-        double[][] haplotypeLikehoodMatrix;
-
-
         for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {
             AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
 
@@ -375,15 +384,14 @@ private HaplotypeIndelErrorModel model;
                 pileup = context.getBasePileup();
 
             if (pileup != null ) {
+                double[] genotypeLikelihoods;
                 if (useOldWrongHorribleHackedUpLikelihoodModel)
-                    haplotypeLikehoodMatrix = model.computeReadHaplotypeLikelihoods( pileup, haplotypesInVC);
+                    genotypeLikelihoods = model.computeReadHaplotypeLikelihoods( pileup, haplotypeMap);
                 else
-                    haplotypeLikehoodMatrix = pairModel.computeReadHaplotypeLikelihoods( pileup, haplotypesInVC, ref, HAPLOTYPE_SIZE, eventLength);
+                    genotypeLikelihoods = pairModel.computeReadHaplotypeLikelihoods( pileup, haplotypeMap, ref, HAPLOTYPE_SIZE, eventLength, indelLikelihoodMap);
 
 
 
-                double[] genotypeLikelihoods = HaplotypeIndelErrorModel.getHaplotypeLikelihoods( haplotypeLikehoodMatrix);
-
                 GLs.put(sample.getKey(), new BiallelicGenotypeLikelihoods(sample.getKey(),
                         refAllele,
                         altAllele,
@@ -398,4 +406,7 @@ private HaplotypeIndelErrorModel model;
 
         return refAllele;
     }
+
+ 
+
 }

java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.AlignmentBlock;
 import net.sf.samtools.SAMRecord;
+import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -37,6 +38,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
 
 public class HaplotypeIndelErrorModel {
@@ -419,7 +421,7 @@ public class HaplotypeIndelErrorModel {
 
     }
 
-    public double[][] computeReadHaplotypeLikelihoods(ReadBackedPileup pileup, List<Haplotype> haplotypesInVC){
+    public double[] computeReadHaplotypeLikelihoods(ReadBackedPileup pileup, HashMap<Allele,Haplotype> haplotypesInVC){
         double[][] haplotypeLikehoodMatrix = new double[haplotypesInVC.size()][haplotypesInVC.size()];
         double readLikelihoods[][] = new double[pileup.getReads().size()][haplotypesInVC.size()];
         int i=0;
@@ -429,7 +431,8 @@ public class HaplotypeIndelErrorModel {
             }
             // for each read/haplotype combination, compute likelihoods, ie -10*log10(Pr(R | Hi))
             // = sum_j(-10*log10(Pr(R_j | Hi) since reads are assumed to be independent
-            for (int j=0; j < haplotypesInVC.size(); j++) {
+            int j=0;
+            for (Allele a: haplotypesInVC.keySet()) {
                 readLikelihoods[i][j]= computeReadLikelihoodGivenHaplotype(haplotypesInVC.get(j), read);
                 if (DEBUG) {
                     System.out.print(read.getReadName()+" ");
@@ -438,7 +441,7 @@ public class HaplotypeIndelErrorModel {
                             read.getUnclippedStart(), read.getAlignmentEnd(), read.getUnclippedEnd(),
                             read.getCigarString(), readLikelihoods[i][j]);
                 }
-
+                j++;
             }
             i++;
         }
@@ -465,11 +468,11 @@ public class HaplotypeIndelErrorModel {
             }
         }
 
-        return haplotypeLikehoodMatrix;
+        return getHaplotypeLikelihoods(haplotypeLikehoodMatrix);
 
     }
 
-    public static double[] getHaplotypeLikelihoods(double[][] haplotypeLikehoodMatrix) {
+    private double[] getHaplotypeLikelihoods(double[][] haplotypeLikehoodMatrix) {
         int hSize = haplotypeLikehoodMatrix.length;
         double[] genotypeLikelihoods = new double[hSize*(hSize+1)/2];
 

java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java

@@ -29,6 +29,7 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
+import org.broad.tribble.util.variantcontext.Allele;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate;
 import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager;
@@ -41,6 +42,7 @@ import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
@@ -48,9 +50,7 @@ import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Arrays;
-import java.util.List;
 import java.util.regex.Pattern;
 
 
@@ -697,29 +697,31 @@ public class PairHMMIndelErrorModel {
 
     }
 
-    private void fillGapProbabilities(int hIndex, int[] hrunProfile,
+    private void fillGapProbabilities(int[] hrunProfile,
-                                      double[][] contextLogGapOpenProbabilities, double[][] contextLogGapContinuationProbabilities) {
+                                      double[] contextLogGapOpenProbabilities, double[] contextLogGapContinuationProbabilities) {
         // fill based on lookup table
         for (int i = 0; i < hrunProfile.length; i++) {
             if (hrunProfile[i] >= MAX_HRUN_GAP_IDX) {
-                contextLogGapOpenProbabilities[hIndex][i] = GAP_OPEN_PROB_TABLE[MAX_HRUN_GAP_IDX-1];
+                contextLogGapOpenProbabilities[i] = GAP_OPEN_PROB_TABLE[MAX_HRUN_GAP_IDX-1];
-                contextLogGapContinuationProbabilities[hIndex][i] = GAP_CONT_PROB_TABLE[MAX_HRUN_GAP_IDX-1];
+                contextLogGapContinuationProbabilities[i] = GAP_CONT_PROB_TABLE[MAX_HRUN_GAP_IDX-1];
             }
             else {
-                contextLogGapOpenProbabilities[hIndex][i] = GAP_OPEN_PROB_TABLE[hrunProfile[i]];
+                contextLogGapOpenProbabilities[i] = GAP_OPEN_PROB_TABLE[hrunProfile[i]];
-                contextLogGapContinuationProbabilities[hIndex][i] = GAP_CONT_PROB_TABLE[hrunProfile[i]];
+                contextLogGapContinuationProbabilities[i] = GAP_CONT_PROB_TABLE[hrunProfile[i]];
             }
         }
     }
-    public synchronized double[][] computeReadHaplotypeLikelihoods(ReadBackedPileup pileup, List<Haplotype> haplotypesInVC,
+    public synchronized double[] computeReadHaplotypeLikelihoods(ReadBackedPileup pileup, LinkedHashMap<Allele,Haplotype> haplotypeMap,
-                                                                   ReferenceContext ref, int haplotypeSize, int eventLength){
+                                                                   ReferenceContext ref, int haplotypeSize, int eventLength,
-        double[][] haplotypeLikehoodMatrix = new double[haplotypesInVC.size()][haplotypesInVC.size()];
+                                                                   HashMap<PileupElement, LinkedHashMap<Allele,Double>> indelLikelihoodMap){
-        double readLikelihoods[][] = new double[pileup.getReads().size()][haplotypesInVC.size()];
+
+        int numHaplotypes = haplotypeMap.size();
+        double[][] haplotypeLikehoodMatrix = new double[numHaplotypes][numHaplotypes];
+        double readLikelihoods[][] = new double[pileup.getReads().size()][numHaplotypes];
         int readIdx=0;
 
-        double[][] contextLogGapOpenProbabilities = null;
+        LinkedHashMap<Allele,double[]> gapOpenProbabilityMap = new LinkedHashMap<Allele,double[]>();
-        double[][] contextLogGapContinuationProbabilities = null;
+        LinkedHashMap<Allele,double[]> gapContProbabilityMap = new LinkedHashMap<Allele,double[]>();
-
 
         if (DEBUG) {
             System.out.println("Reference bases:");
@@ -727,15 +729,15 @@ public class PairHMMIndelErrorModel {
         }
 
         if (doContextDependentPenalties && !getGapPenaltiesFromFile)   {
-            // will context dependent probabilities based on homopolymet run. Probabilities are filled based on total complete haplotypes.
+            // will context dependent probabilities based on homopolymer run. Probabilities are filled based on total complete haplotypes.
 
-            for (int j=0; j < haplotypesInVC.size(); j++) {
+
-                Haplotype haplotype = haplotypesInVC.get(j);
+            for (Allele a: haplotypeMap.keySet()) {
+                Haplotype haplotype = haplotypeMap.get(a);
                 byte[] haplotypeBases = haplotype.getBasesAsBytes();
-                if (contextLogGapOpenProbabilities == null) {
+                double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length];
-                    contextLogGapOpenProbabilities = new double[haplotypesInVC.size()][haplotypeBases.length];
+                double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length];
-                    contextLogGapContinuationProbabilities = new double[haplotypesInVC.size()][haplotypeBases.length];
+
-                }
                 // get homopolymer length profile for current haplotype
                 int[] hrunProfile = new int[haplotypeBases.length];
                 getContextHomopolymerLength(haplotypeBases,hrunProfile);
@@ -746,12 +748,25 @@ public class PairHMMIndelErrorModel {
                         System.out.format("%d",hrunProfile[i]);
                     System.out.println();
                 }
-                fillGapProbabilities(j, hrunProfile, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities);
+                fillGapProbabilities(hrunProfile, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities);
+
+                gapOpenProbabilityMap.put(a,contextLogGapOpenProbabilities);
+                gapContProbabilityMap.put(a,contextLogGapContinuationProbabilities);
 
             }
         }
-        for (SAMRecord pread : pileup.getReads()) {
+        for (PileupElement p: pileup) {
-            GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(pread);
+
+            // check if we've already computed likelihoods for this pileup element (i.e. for this read at this location)
+            if (indelLikelihoodMap.containsKey(p)) {
+                HashMap<Allele,Double> el =  indelLikelihoodMap.get(p);
+                int j=0;
+                for (Allele a: haplotypeMap.keySet()) {
+                    readLikelihoods[readIdx][j++] = el.get(a);
+                }
+            }
+            else {
+                GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
                 if (read == null)
                     continue;
 
@@ -760,6 +775,8 @@ public class PairHMMIndelErrorModel {
                 }
 
                 double[] recalQuals = null;
+
+
                 if (getGapPenaltiesFromFile) {
                     RecalDataManager.parseSAMRecord( read, RAC );
 
@@ -823,7 +840,7 @@ public class PairHMMIndelErrorModel {
                 numEndSoftClippedBases = read.getUnclippedEnd()- read.getAlignmentEnd();
 
                 // check for hard clips (never consider these bases):
-/*            Cigar c = read.getCigar();
+    /*            Cigar c = read.getCigar();
                 CigarElement first = c.getCigarElement(0);
                 CigarElement last = c.getCigarElement(c.numCigarElements()-1);
                 int numStartHardClippedBases = 0, numEndHardClippedBases = 0;
@@ -903,13 +920,18 @@ public class PairHMMIndelErrorModel {
 
 
 
+                LinkedHashMap<Allele,Double> readEl = new LinkedHashMap<Allele,Double>();
+
                 if (numStartClippedBases + numEndClippedBases >= unclippedReadBases.length) {
                     if (DEBUG)
                         System.out.println("BAD READ!!");
 
-                for (int j=0; j < haplotypesInVC.size(); j++) {
+                    int j=0;
-                    readLikelihoods[readIdx][j]= 0;
+                    for (Allele a: haplotypeMap.keySet()) {
+                        readEl.put(a,0.0);
+                        readLikelihoods[readIdx][j++] = 0.0;
                     }
+
                 }
                 else {
                     byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartClippedBases,
@@ -930,12 +952,11 @@ public class PairHMMIndelErrorModel {
                         System.out.println(new String(readBases));
                     }
 
+                    int j=0;
+                    for (Allele a: haplotypeMap.keySet()) {
 
-                // start and stop have indices into
-
-                for (int j=0; j < haplotypesInVC.size(); j++) {
-                    Haplotype haplotype = haplotypesInVC.get(j);
 
+                        Haplotype haplotype = haplotypeMap.get(a);
                         if (stop > haplotype.getStopPosition())
                             stop = haplotype.getStopPosition();
 
@@ -954,6 +975,7 @@ public class PairHMMIndelErrorModel {
                             System.out.println(new String(haplotypeBases));
                         }
 
+                        Double readLikelihood = 0.0;
                         if (useAffineGapModel) {
 
                             double[] currentContextGOP = null;
@@ -962,23 +984,25 @@ public class PairHMMIndelErrorModel {
                             if (doContextDependentPenalties) {
 
                                if (getGapPenaltiesFromFile) {
-                               readLikelihoods[readIdx][j]= computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, recalCDP, null);
+                                   readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, recalCDP, null);
 
                                }  else {
-                               currentContextGOP = Arrays.copyOfRange(contextLogGapOpenProbabilities[j], (int)indStart, (int)indStop);
+                                   currentContextGOP = Arrays.copyOfRange(gapOpenProbabilityMap.get(a), (int)indStart, (int)indStop);
-                               currentContextGCP = Arrays.copyOfRange(contextLogGapContinuationProbabilities[j], (int)indStart, (int)indStop);
+                                   currentContextGCP = Arrays.copyOfRange(gapContProbabilityMap.get(a), (int)indStart, (int)indStop);
-                               readLikelihoods[readIdx][j]= computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, currentContextGOP, currentContextGCP);
+                                   readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, currentContextGOP, currentContextGCP);
                                }
                             }
 
                         }
                         else
-                        readLikelihoods[readIdx][j]= computeReadLikelihoodGivenHaplotype(haplotypeBases, readBases, readQuals);
+                            readLikelihood = computeReadLikelihoodGivenHaplotype(haplotypeBases, readBases, readQuals);
-
 
+                        readEl.put(a,readLikelihood);
+                        readLikelihoods[readIdx][j++] = readLikelihood;
                     }
                 }
-
+                indelLikelihoodMap.put(p,readEl);
+            }
             readIdx++;
         }
 
@@ -992,8 +1016,8 @@ public class PairHMMIndelErrorModel {
             }
 
         }
-        for (int i=0; i < haplotypesInVC.size(); i++) {
+        for (int i=0; i < numHaplotypes; i++) {
-            for (int j=i; j < haplotypesInVC.size(); j++){
+            for (int j=i; j < numHaplotypes; j++){
                 // combine likelihoods of haplotypeLikelihoods[i], haplotypeLikelihoods[j]
                 // L(Hi, Hj) = sum_reads ( Pr(R|Hi)/2 + Pr(R|Hj)/2)
                 //readLikelihoods[k][j] has log10(Pr(R_k) | H[j] )
@@ -1002,7 +1026,7 @@ public class PairHMMIndelErrorModel {
 
                     // Compute log10(10^x1/2 + 10^x2/2) = log10(10^x1+10^x2)-log10(2)
                     // First term is approximated by Jacobian log with table lookup.
-                    if (Double.isInfinite(readLikelihoods[readIdx][i]) || Double.isInfinite(readLikelihoods[readIdx][j]))
+                    if (Double.isInfinite(readLikelihoods[readIdx][i]) && Double.isInfinite(readLikelihoods[readIdx][j]))
                         continue;
                     haplotypeLikehoodMatrix[i][j] += ( MathUtils.softMax(readLikelihoods[readIdx][i],
                             readLikelihoods[readIdx][j]) + LOG_ONE_HALF);
@@ -1013,7 +1037,7 @@ public class PairHMMIndelErrorModel {
             }
         }
 
-        return haplotypeLikehoodMatrix;
+        return getHaplotypeLikelihoods(haplotypeLikehoodMatrix);
 
     }
 

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

@@ -31,9 +31,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Arrays;
-import java.util.List;
 
 public class Haplotype {
     protected byte[] bases = null;
@@ -108,11 +106,11 @@ public class Haplotype {
         return isReference;
     }
 
-    public static List<Haplotype> makeHaplotypeListFromAlleles(List<Allele> alleleList, int startPos, ReferenceContext ref,
+    public static LinkedHashMap<Allele,Haplotype> makeHaplotypeListFromAlleles(List<Allele> alleleList, int startPos, ReferenceContext ref,
                                                                final int haplotypeSize, final int numPrefBases) {
 
 
-        List<Haplotype> haplotypeList = new ArrayList<Haplotype>();
+        LinkedHashMap<Allele,Haplotype> haplotypeMap = new LinkedHashMap<Allele,Haplotype>();
 
         Allele refAllele = null;
 
@@ -153,11 +151,11 @@ public class Haplotype {
             String haplotypeString = new String(basesBeforeVariant) + new String(alleleBases) + new String(basesAfterVariant);
             haplotypeString = haplotypeString.substring(0,haplotypeSize);
 
-           haplotypeList.add(new Haplotype(haplotypeString.getBytes(), locus, a.isReference()));
+           haplotypeMap.put(a,new Haplotype(haplotypeString.getBytes(), locus, a.isReference()));
 
         }
 
-        return haplotypeList;
+        return haplotypeMap;
     }
 
 }