+++ /dev/null
-#include <stdio.h>
-#include <stdlib.h>
-#include <ctype.h>
-#include <assert.h>
-#include "sam.h"
-
-typedef struct __linkbuf_t {
- bam1_t b;
- uint32_t beg, end;
- struct __linkbuf_t *next;
-} lbnode_t;
-
-/* --- BEGIN: Memory pool */
-
-typedef struct {
- int cnt, n, max;
- lbnode_t **buf;
-} mempool_t;
-
-static mempool_t *mp_init()
-{
- mempool_t *mp;
- mp = (mempool_t*)calloc(1, sizeof(mempool_t));
- return mp;
-}
-static void mp_destroy(mempool_t *mp)
-{
- int k;
- for (k = 0; k < mp->n; ++k) {
- free(mp->buf[k]->b.data);
- free(mp->buf[k]);
- }
- free(mp->buf);
- free(mp);
-}
-static inline lbnode_t *mp_alloc(mempool_t *mp)
-{
- ++mp->cnt;
- if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
- else return mp->buf[--mp->n];
-}
-static inline void mp_free(mempool_t *mp, lbnode_t *p)
-{
- --mp->cnt; p->next = 0; // clear lbnode_t::next here
- if (mp->n == mp->max) {
- mp->max = mp->max? mp->max<<1 : 256;
- mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
- }
- mp->buf[mp->n++] = p;
-}
-
-/* --- END: Memory pool */
-
-/* --- BEGIN: Auxiliary functions */
-
-static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
-{
- unsigned k;
- bam1_t *b = p->b;
- bam1_core_t *c = &b->core;
- uint32_t x = c->pos, y = 0;
- int ret = 1, is_restart = 1;
-
- 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;
- 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 (op == BAM_CMATCH) { // NOTE: this assumes the first and the last operation MUST BE a match or a clip
- 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 + l - 1 == pos) { // come to the end of a match
- 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) 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
- 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
- }
- }
- }
- }
- x += l; y += l;
- } else if (op == BAM_CDEL) { // then set ->is_del
- if (x + l > pos) {
- p->indel = 0; p->is_del = 1;
- p->qpos = y + (pos - x);
- }
- x += l;
- } else if (op == BAM_CREF_SKIP) x += l;
- else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
- 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;
- }
- }
- assert(x > pos); // otherwise a bug
- return ret;
-}
-
-/* --- END: Auxiliary functions */
-
-/*******************
- * pileup iterator *
- *******************/
-
-struct __bam_plp_t {
- mempool_t *mp;
- lbnode_t *head, *tail, *dummy;
- int32_t tid, pos, max_tid, max_pos;
- 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(bam_plp_auto_f func, void *data)
-{
- bam_plp_t iter;
- iter = calloc(1, sizeof(struct __bam_plp_t));
- iter->mp = mp_init();
- iter->head = iter->tail = mp_alloc(iter->mp);
- 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;
-}
-
-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)) {
- int n_plp = 0;
- lbnode_t *p, *q;
- // write iter->plp at iter->pos
- iter->dummy->next = iter->head;
- for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
- if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
- q->next = p->next; mp_free(iter->mp, p); p = q;
- } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
- if (n_plp == iter->max_plp) { // then double the capacity
- iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
- iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
- }
- iter->plp[n_plp].b = &p->b;
- if (resolve_cigar(iter->plp + n_plp, iter->pos)) ++n_plp; // skip the read if we are looking at ref-skip
- }
- }
- iter->head = iter->dummy->next; // dummy->next may be changed
- *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
- // update iter->tid and 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;
- }
- }
- if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
- iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
- } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
- iter->pos = iter->head->beg; // jump to the next position
- } else ++iter->pos; // scan contiguously
- // return
- if (n_plp) return iter->plp;
- if (iter->is_eof && iter->head->next == 0) break;
- }
- 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;
- bam_copy1(&iter->tail->b, b);
- 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;
- if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
- iter->tail->next = mp_alloc(iter->mp);
- iter->tail = iter->tail->next;
- }
- } else iter->is_eof = 1;
- 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->max_tid = iter->max_pos = -1;
- iter->tid = iter->pos = 0;
- iter->is_eof = 0;
- for (p = iter->head; p->next;) {
- q = p->next;
- mp_free(iter->mp, p);
- p = q;
- }
- iter->head = iter->tail;
-}
-
-void bam_plp_set_mask(bam_plp_t iter, int mask)
-{
- iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
-}
-
-/*****************
- * callback APIs *
- *****************/
-
-int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
-{
- bam_plbuf_t *buf;
- int ret;
- bam1_t *b;
- b = bam_init1();
- buf = bam_plbuf_init(func, func_data);
- bam_plbuf_set_mask(buf, mask);
- while ((ret = bam_read1(fp, b)) >= 0)
- bam_plbuf_push(b, buf);
- bam_plbuf_push(0, buf);
- bam_plbuf_destroy(buf);
- bam_destroy1(b);
- return 0;
-}
-
-void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
-{
- bam_plp_set_mask(buf->iter, mask);
-}
-
-void bam_plbuf_reset(bam_plbuf_t *buf)
-{
- bam_plp_reset(buf->iter);
-}
-
-bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
-{
- bam_plbuf_t *buf;
- buf = calloc(1, sizeof(bam_plbuf_t));
- buf->iter = bam_plp_init(0, 0);
- buf->func = func;
- buf->data = data;
- return buf;
-}
-
-void bam_plbuf_destroy(bam_plbuf_t *buf)
-{
- bam_plp_destroy(buf->iter);
- free(buf);
-}
-
-int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
-{
- int ret, n_plp, tid, pos;
- const bam_pileup1_t *plp;
- ret = bam_plp_push(buf->iter, b);
- if (ret < 0) return ret;
- 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;
-}
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