- if (_cop(cigar[0]) == BAM_CMATCH) s->k = 0, s->x = c->pos, s->y = 0;
- } else { // find the first match
+ if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
+ } else { // find the first match or deletion