return -1;
}
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) {
+ if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[0]);
+ } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
write_cigar(cigar2, n2, m2, cigar[0]);
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);
} else ++k;
}
write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
- if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
- if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+ if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
}
write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
}
- /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */
+ /* 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]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
- cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;
+ 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)) {
+ /* This is a redundant P operator */
+ cigar2[i-1] = 0; // i.e. 0M
+ /* If had same operator either side, combine them in post_op */
+ if (pre_op == post_op) {
+ /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+ cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+ cigar2[i-2] = 0; // i.e. 0M
+ }
+ }
+ }
+ /* Remove the zero'd operators (0M) */
for (i = k = 0; i < n2; ++i)
if (cigar2[i]) cigar2[k++] = cigar2[i];
n2 = k;