int32_t l = 0;
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
+ if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
l += cigar[k] >> BAM_CIGAR_SHIFT;
}
return l;
else {
for (i = 0; i < c->n_cigar; ++i) {
kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
- kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+ kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
}
}
kputc('\t', &str);