pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (pileup == null)
return null;
<BUG>final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus);
</BUG>
final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage();
if (haplotypes != null) {
final Set<Map.Entry<String, Genotype>> genotypes = vc.getGenotypes().entrySet();

pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (pileup == null)
return null;
final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus, vc);
final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage();
if (haplotypes != null) {
final Set<Map.Entry<String, Genotype>> genotypes = vc.getGenotypes().entrySet();
