if ( allele.isNoCall() ) {
continue; // this does not look so good, should we die???
}
alleleCounts.put(getAlleleRepresentation(allele), 0);
}
<BUG>for ( ExtendedEventPileupElement e : pileup.toExtendedIterable() ) {
if ( e.isInsertion() ) {

final String b =  e.getEventBases();
</BUG>
if ( alleleCounts.containsKey(b) ) {

if ( allele.isNoCall() ) {
continue; // this does not look so good, should we die???
}
alleleCounts.put(getAlleleRepresentation(allele), 0);
}
for ( PileupElement p : pileup ) {
if ( p.isBeforeInsertion() ) {
final String b = p.getEventBases();
if ( alleleCounts.containsKey(b) ) {
