<BUG>}
ReadBackedExtendedEventPileup pileup = stratifiedContext.getExtendedEventPileup();
</BUG>
if ( pileup == null )
return null;
<BUG>HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>();

alleleCounts.put(REF_ALLELE,0);

Allele refAllele = vc.getReference();
</BUG>
for ( Allele allele : vc.getAlternateAlleles() ) {

Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), counts);
return map;
}
private Map<String,Object> annotateIndel(AlignmentContext stratifiedContext, VariantContext vc) {
if ( ! stratifiedContext.hasBasePileup() )
return null;
ReadBackedPileup pileup = stratifiedContext.getBasePileup();
if ( pileup == null )
return null;
final HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>();
alleleCounts.put(REF_ALLELE, 0);
final Allele refAllele = vc.getReference();
for ( Allele allele : vc.getAlternateAlleles() ) {
