if ( vc.isIndel() )
return annotateIndel(stratifiedContext, vc);
return null;
}
private Map<String,Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) {
<BUG>if ( ! stratifiedContext.hasBasePileup() ) return null;
HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();</BUG>
for ( Allele allele : vc.getAlleles() )
alleleCounts.put(allele.getBases()[0], 0);
ReadBackedPileup pileup = stratifiedContext.getBasePileup();

if ( vc.isIndel() )
return annotateIndel(stratifiedContext, vc);
return null;
}
private Map<String,Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) {
if ( ! stratifiedContext.hasBasePileup() )
return null;
HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
for ( Allele allele : vc.getAlleles() )
alleleCounts.put(allele.getBases()[0], 0);
ReadBackedPileup pileup = stratifiedContext.getBasePileup();
