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;
mempool_t *mp;
lbnode_t *head, *tail, *dummy;
int32_t tid, pos, max_tid, max_pos;
- int is_eof, flag_mask, max_plp;
+ int is_eof, flag_mask, max_plp, error;
bam_pileup1_t *plp;
+ // for the "auto" interface only
+ bam1_t *b;
+ bam_plp_auto_f func;
+ void *data;
};
-bam_plp_t bam_plp_init(void)
+bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
{
bam_plp_t iter;
iter = calloc(1, sizeof(struct __bam_plp_t));
iter->dummy = mp_alloc(iter->mp);
iter->max_tid = iter->max_pos = -1;
iter->flag_mask = BAM_DEF_MASK;
+ if (func) {
+ iter->func = func;
+ iter->data = data;
+ iter->b = bam_init1();
+ }
return iter;
}
-const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_n_plp, int *_tid, int *_pos)
+void bam_plp_destroy(bam_plp_t iter)
+{
+ mp_free(iter->mp, iter->dummy);
+ mp_free(iter->mp, iter->head);
+ if (iter->mp->cnt != 0)
+ fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
+ mp_destroy(iter->mp);
+ if (iter->b) bam_destroy1(iter->b);
+ free(iter->plp);
+ free(iter);
+}
+
+const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
{
+ if (iter->error) { *_n_plp = -1; return 0; }
*_n_plp = 0;
if (iter->is_eof && iter->head->next == 0) return 0;
while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
if (iter->head->next) {
if (iter->tid > iter->head->b.core.tid) {
fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
+ iter->error = 1;
*_n_plp = -1;
return 0;
}
int bam_plp_push(bam_plp_t iter, const bam1_t *b)
{
+ if (iter->error) return -1;
if (b) {
if (b->core.tid < 0) return 0;
if (b->core.flag & iter->flag_mask) return 0;
iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
if (b->core.tid < iter->max_tid) {
fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
+ iter->error = 1;
return -1;
}
if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
+ iter->error = 1;
return -1;
}
iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
return 0;
}
+const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+{
+ const bam_pileup1_t *plp;
+ if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
+ if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+ else {
+ *_n_plp = 0;
+ if (iter->is_eof) return 0;
+ while (iter->func(iter->data, iter->b) >= 0) {
+ if (bam_plp_push(iter, iter->b) < 0) {
+ *_n_plp = -1;
+ return 0;
+ }
+ if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+ }
+ bam_plp_push(iter, 0);
+ if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+ return 0;
+ }
+}
+
void bam_plp_reset(bam_plp_t iter)
{
lbnode_t *p, *q;
iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
}
-void bam_plp_destroy(bam_plp_t iter)
-{
- mp_free(iter->mp, iter->dummy);
- mp_free(iter->mp, iter->head);
- if (iter->mp->cnt != 0)
- fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
- mp_destroy(iter->mp);
- free(iter->plp);
- free(iter);
-}
-
/*****************
* callback APIs *
*****************/
{
bam_plbuf_t *buf;
buf = calloc(1, sizeof(bam_plbuf_t));
- buf->iter = bam_plp_init();
+ buf->iter = bam_plp_init(0, 0);
buf->func = func;
buf->data = data;
return buf;
const bam_pileup1_t *plp;
ret = bam_plp_push(buf->iter, b);
if (ret < 0) return ret;
- while ((plp = bam_plp_next(buf->iter, &n_plp, &tid, &pos)) != 0)
+ while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
buf->func(tid, pos, n_plp, plp, buf->data);
return 0;
}
+
+/***********
+ * mpileup *
+ ***********/
+
+struct __bam_mplp_t {
+ int n;
+ uint64_t min, *pos;
+ bam_plp_t *iter;
+ int *n_plp;
+ const bam_pileup1_t **plp;
+};
+
+bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
+{
+ int i;
+ bam_mplp_t iter;
+ iter = calloc(1, sizeof(struct __bam_mplp_t));
+ iter->pos = calloc(n, 8);
+ iter->n_plp = calloc(n, sizeof(int));
+ iter->plp = calloc(n, sizeof(void*));
+ iter->iter = calloc(n, sizeof(void*));
+ iter->n = n;
+ iter->min = (uint64_t)-1;
+ for (i = 0; i < n; ++i) {
+ iter->iter[i] = bam_plp_init(func, data[i]);
+ iter->pos[i] = iter->min;
+ }
+ return iter;
+}
+
+void bam_mplp_destroy(bam_mplp_t iter)
+{
+ int i;
+ for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
+ free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
+ free(iter);
+}
+
+int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
+{
+ int i, ret = 0;
+ uint64_t new_min = (uint64_t)-1;
+ for (i = 0; i < iter->n; ++i) {
+ if (iter->pos[i] == iter->min) {
+ int tid, pos;
+ iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
+ iter->pos[i] = (uint64_t)tid<<32 | pos;
+ }
+ if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
+ }
+ iter->min = new_min;
+ if (new_min == (uint64_t)-1) return 0;
+ *_tid = new_min>>32; *_pos = (uint32_t)new_min;
+ for (i = 0; i < iter->n; ++i) {
+ if (iter->pos[i] == iter->min) {
+ n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
+ ++ret;
+ } else n_plp[i] = 0, plp[i] = 0;
+ }
+ return ret;
+}
projects / samtools.git / blobdiff