* CIGAR related routines *
**************************/
-int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg)
+int bam_tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int32_t *_tpos)
{
- unsigned k;
- int32_t x = c->pos, y = 0;
- int state = 0;
+ int k, x = c->pos, y = 0, last_y = 0;
+ *_tpos = c->pos;
for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK; // operation
- int l = cigar[k] >> BAM_CIGAR_SHIFT; // length
- if (state == 0 && (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CINS) && x + l > pos) {
- reg->tbeg = x; reg->qbeg = y; reg->cbeg = k;
- state = 1;
- }
- if (op == BAM_CMATCH) { x += l; y += l; }
- else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
- else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
- if (state == 1 && (op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP || op == BAM_CREF_SKIP || k == c->n_cigar - 1)) {
- reg->tend = x; reg->qend = y; reg->cend = k;
+ int op = cigar[k] & BAM_CIGAR_MASK;
+ int l = cigar[k] >> BAM_CIGAR_SHIFT;
+ if (op == BAM_CMATCH) {
+ if (c->pos > tpos) return y;
+ if (x + l > tpos) {
+ *_tpos = tpos;
+ return y + (tpos - x);
+ }
+ x += l; y += l;
+ last_y = y;
+ } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+ if (x + l > tpos) {
+ *_tpos = x;
+ return y;
+ }
+ x += l;
}
}
- return state? 0 : -1;
+ *_tpos = x;
+ return last_y;
}
uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)