for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
} else if (op == BAM_CSOFT_CLIP) {
j += ol;
+ } else if (op == BAM_CHARD_CLIP) {
+ /* do nothing */
} else if (op == BAM_CDEL || op == BAM_CPAD) {
for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
} else {
}
unpad_seq(b, &q);
if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+ if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[0]);
+ if (bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[1]);
+ }
/* Include any pads if starts with an insert */
for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));