44ac49aa346d6757b41fe99d40930dd271df7fcd,public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java,HaplotypeScore,annotate,#RefMetaDataTracker#AnnotatorCompatibleWalker#ReferenceContext#Map#VariantContext#,63
Before Change
// Compute all haplotypes consistent with the current read pileup
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, vc);
After Change
final int locus = ref.getLocus().getStart() + (ref.getLocus().getStop() - ref.getLocus().getStart()) / 2;
if ( !context.hasBasePileup() )
return null;
final ReadBackedPileup pileup = context.getBasePileup();
// Compute all haplotypes consistent with the current read pileup
final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus, vc);