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Bug fix: inbreeding coeff shouldn't be computed in ref-only sites

This commit is contained in:
Guillermo del Angel 2012-10-18 15:42:14 -04:00
parent b57df6cac8
commit 3db38c5a93
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
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@ -48,7 +48,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
private Map<String, Object> calculateIC(final VariantContext vc) { private Map<String, Object> calculateIC(final VariantContext vc) {
final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds); final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds);
if ( genotypes == null || genotypes.size() < MIN_SAMPLES ) if ( genotypes == null || genotypes.size() < MIN_SAMPLES || !vc.isVariant())
return null; return null;
int idxAA = 0, idxAB = 1, idxBB = 2; int idxAA = 0, idxAB = 1, idxBB = 2;