final String b = DEL;
if ( alleleCounts.containsKey(b) ) {
alleleCounts.put(b, alleleCounts.get(b)+1);
}
}
<BUG>}
else {
if ( e.getRead().getAlignmentEnd() <= vc.getStart() ) {

continue;
}
alleleCounts.put(REF_ALLELE,alleleCounts.get(REF_ALLELE)+1);

}</BUG>
}

final String b = DEL;
if ( alleleCounts.containsKey(b) ) {
alleleCounts.put(b, alleleCounts.get(b)+1);
