
final String b =  e.getEventBases();
</BUG>
if ( alleleCounts.containsKey(b) ) {
alleleCounts.put(b, alleleCounts.get(b)+1);
<BUG>}
} else {
if ( e.isDeletion() ) {
if ( e.getEventLength() == refAllele.length() ) {
</BUG>
final String b = DEL;

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) ) {
alleleCounts.put(b, alleleCounts.get(b)+1);
}
} else if ( p.isBeforeDeletionStart() ) {
if ( p.getEventLength() == refAllele.length() ) {
final String b = DEL;
