bam1_t *b = p->b;
bam1_core_t *c = &b->core;
uint32_t x = c->pos, y = 0;
- int ret = 1, is_restart = 1;
+ int ret = 1, is_restart = 1, first_op, last_op;
if (c->flag&BAM_FUNMAP) return 0; // unmapped read
assert(x <= pos); // otherwise a bug
p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0;
+ first_op = bam1_cigar(b)[0] & BAM_CIGAR_MASK;
+ last_op = bam1_cigar(b)[c->n_cigar-1] & BAM_CIGAR_MASK;
for (k = 0; k < c->n_cigar; ++k) {
int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
if (x + l > pos) { // overlap with pos
p->indel = p->is_del = 0;
p->qpos = y + (pos - x);
- if (x == pos && is_restart) p->is_head = 1;
+ if (x == pos && is_restart && first_op != BAM_CDEL) p->is_head = 1;
if (x + l - 1 == pos) { // come to the end of a match
- if (k < c->n_cigar - 1) { // there are additional operation(s)
+ int has_next_match = 0;
+ unsigned i;
+ for (i = k + 1; i < c->n_cigar; ++i) {
+ uint32_t cigar = bam1_cigar(b)[i];
+ int opi = cigar&BAM_CIGAR_MASK;
+ if (opi == BAM_CMATCH) {
+ has_next_match = 1;
+ break;
+ } else if (opi == BAM_CSOFT_CLIP || opi == BAM_CREF_SKIP || opi == BAM_CHARD_CLIP) break;
+ }
+ if (!has_next_match && last_op != BAM_CDEL) p->is_tail = 1;
+ if (k < c->n_cigar - 1 && has_next_match) { // there are additional operation(s)
uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR
int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
- if (op_next == BAM_CDEL || op_next == BAM_CINS) {
- if (k + 2 < c->n_cigar) op_next = bam1_cigar(b)[k+2]&BAM_CIGAR_MASK;
- else p->is_tail = 1;
+ else if (op_next == BAM_CPAD && k + 2 < c->n_cigar) { // no working for adjacent padding
+ cigar = bam1_cigar(b)[k+2]; op_next = cigar&BAM_CIGAR_MASK;
+ if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
+ else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
}
- if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP)
- p->is_tail = 1; // tail
- } else p->is_tail = 1; // this is the last operation; set tail
+ }
}
}
x += l; y += l;
} else if (op == BAM_CDEL) { // then set ->is_del
+ if (k == 0 && x == pos) p->is_head = 1;
+ else if (x + l - 1 == pos && k == c->n_cigar - 1) p->is_tail = 1;
if (x + l > pos) {
p->indel = 0; p->is_del = 1;
- p->qpos = y + (pos - x);
+ p->qpos = y;
}
x += l;
} else if (op == BAM_CREF_SKIP) x += l;
else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
- is_restart = (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
+ if (is_restart) is_restart ^= (op == BAM_CMATCH);
+ else is_restart ^= (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
if (x > pos) {
if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all
break;