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Necessary changes to enable HaplotypeScore annotation for indels 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4974 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-01-12 01:09:12 +00:00
parent 23597a2bde
commit bdd382198c
1 changed files with 24 additions and 4 deletions
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28
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -57,7 +57,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
}
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
if ( !vc.isBiallelic() || !vc.isSNP() || stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
if ( !vc.isBiallelic() || stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
return null;
final AlignmentContext context = StratifiedAlignmentContext.joinContexts(stratifiedContexts.values());
@ -68,7 +68,16 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
final int locus = ref.getLocus().getStart() + (ref.getLocus().getStop() - ref.getLocus().getStart()) / 2;
// Compute all haplotypes consistent with the current read pileup
final List<Haplotype> haplotypes = computeHaplotypes(context.getBasePileup(), contextSize, locus);
ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup())
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (pileup == null)
return null;
final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus);
final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage();
if (haplotypes != null) {
@ -76,8 +85,19 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
for ( final Map.Entry<String, Genotype> genotype : genotypes ) {
final StratifiedAlignmentContext thisContext = stratifiedContexts.get(genotype.getKey());
if ( thisContext != null ) {
double thisScore = scoreReadsAgainstHaplotypes(haplotypes, thisContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), contextSize, locus);
scoreRA.add(thisScore); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
final AlignmentContext aContext = thisContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
final ReadBackedPileup thisPileup;
if (aContext.hasExtendedEventPileup())
thisPileup = aContext.getExtendedEventPileup();
else if (aContext.hasBasePileup())
thisPileup = aContext.getBasePileup();
else
thisPileup = null;
if (thisPileup != null) {
double thisScore = scoreReadsAgainstHaplotypes(haplotypes, thisPileup, contextSize, locus);
scoreRA.add(thisScore); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
}
}
}
}