for (final Genotype genotype : genotypes.iterateInSampleNameOrder()) {
final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
if (context == null) {
continue;
}
<BUG>ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup())
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())

pileup = context.getBasePileup();
if (pileup == null)</BUG>
continue;

for (final Genotype genotype : genotypes.iterateInSampleNameOrder()) {
final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
if (context == null) {
continue;
}
if (!context.hasBasePileup())
continue;
final ReadBackedPileup pileup = context.getBasePileup();
if (pileup == null)
continue;
