if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
write_cigar(cigar2, n2, m2, cigar[1]);
}
- } else {
- /* Insert a dummy 0M entry to let use remove superfluous leading P ops */
- write_cigar(cigar2, n2, m2, 0);
}
- /* 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));
/* Determine CIGAR operator for each base in the aligned read */
for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+ /* Include any pads if starts with an insert */
+ if (q.s[0] == BAM_CINS) {
+ 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));
+ }
/* Count consecutive CIGAR operators to turn into a CIGAR string */
for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
if (op != q.s[i]) {
write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
}
/* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
- /* or right at the start before M/X/=/D */
int pre_op, post_op;
for (i = 2; i < n2; ++i)
if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
pre_op = bam_cigar_op(cigar2[i-2]);
post_op = bam_cigar_op(cigar2[i]);
/* Note don't need to check for X/= as code above will use M only */
- if ((pre_op == BAM_CMATCH || pre_op == BAM_CDIFF || pre_op == BAM_CSOFT_CLIP || pre_op == BAM_CHARD_CLIP) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
+ if ((pre_op == BAM_CMATCH || pre_op == BAM_CDIFF) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
/* This is a redundant P operator */
cigar2[i-1] = 0; // i.e. 0M
/* If had same operator either side, combine them in post_op */