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);