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view SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam_pileup.c @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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#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 if (k < c->n_cigar - 1) { // 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; } 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 (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; 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 */ struct __bam_plbuf_t { mempool_t *mp; lbnode_t *head, *tail, *dummy; bam_pileup_f func; void *func_data; int32_t tid, pos, max_tid, max_pos; int max_pu, is_eof; bam_pileup1_t *pu; int flag_mask; }; void bam_plbuf_reset(bam_plbuf_t *buf) { lbnode_t *p, *q; buf->max_tid = buf->max_pos = -1; buf->tid = buf->pos = 0; buf->is_eof = 0; for (p = buf->head; p->next;) { q = p->next; mp_free(buf->mp, p); p = q; } buf->head = buf->tail; } void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask) { if (mask < 0) buf->flag_mask = BAM_DEF_MASK; else buf->flag_mask = BAM_FUNMAP | mask; } bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data) { bam_plbuf_t *buf; buf = (bam_plbuf_t*)calloc(1, sizeof(bam_plbuf_t)); buf->func = func; buf->func_data = data; buf->mp = mp_init(); buf->head = buf->tail = mp_alloc(buf->mp); buf->dummy = mp_alloc(buf->mp); buf->max_tid = buf->max_pos = -1; buf->flag_mask = BAM_DEF_MASK; return buf; } void bam_plbuf_destroy(bam_plbuf_t *buf) { mp_free(buf->mp, buf->dummy); mp_free(buf->mp, buf->head); if (buf->mp->cnt != 0) fprintf(stderr, "[bam_plbuf_destroy] memory leak: %d. Continue anyway.\n", buf->mp->cnt); mp_destroy(buf->mp); free(buf->pu); free(buf); } int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf) { if (b) { // fill buffer if (b->core.tid < 0) return 0; if (b->core.flag & buf->flag_mask) return 0; bam_copy1(&buf->tail->b, b); buf->tail->beg = b->core.pos; buf->tail->end = bam_calend(&b->core, bam1_cigar(b)); if (b->core.tid < buf->max_tid) { fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n"); return -1; } if ((b->core.tid == buf->max_tid) && (buf->tail->beg < buf->max_pos)) { fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n"); return -1; } buf->max_tid = b->core.tid; buf->max_pos = buf->tail->beg; if (buf->tail->end > buf->pos || buf->tail->b.core.tid > buf->tid) { buf->tail->next = mp_alloc(buf->mp); buf->tail = buf->tail->next; } } else buf->is_eof = 1; while (buf->is_eof || buf->max_tid > buf->tid || (buf->max_tid == buf->tid && buf->max_pos > buf->pos)) { int n_pu = 0; lbnode_t *p, *q; buf->dummy->next = buf->head; for (p = buf->head, q = buf->dummy; p->next; q = p, p = p->next) { if (p->b.core.tid < buf->tid || (p->b.core.tid == buf->tid && p->end <= buf->pos)) { // then remove from the list q->next = p->next; mp_free(buf->mp, p); p = q; } else if (p->b.core.tid == buf->tid && p->beg <= buf->pos) { // here: p->end > pos; then add to pileup if (n_pu == buf->max_pu) { // then double the capacity buf->max_pu = buf->max_pu? buf->max_pu<<1 : 256; buf->pu = (bam_pileup1_t*)realloc(buf->pu, sizeof(bam_pileup1_t) * buf->max_pu); } buf->pu[n_pu].b = &p->b; if (resolve_cigar(buf->pu + n_pu, buf->pos)) ++n_pu; // skip the read if we are looking at BAM_CREF_SKIP } } buf->head = buf->dummy->next; // dummy->next may be changed if (n_pu) { // then call user defined function buf->func(buf->tid, buf->pos, n_pu, buf->pu, buf->func_data); } // update tid and pos if (buf->head->next) { if (buf->tid > buf->head->b.core.tid) { fprintf(stderr, "[bam_plbuf_push] unsorted input. Pileup aborts.\n"); return 1; } } if (buf->tid < buf->head->b.core.tid) { // come to a new reference sequence buf->tid = buf->head->b.core.tid; buf->pos = buf->head->beg; // jump to the next reference } else if (buf->pos < buf->head->beg) { // here: tid == head->b.core.tid buf->pos = buf->head->beg; // jump to the next position } else ++buf->pos; // scan contiguously if (buf->is_eof && buf->head->next == 0) break; } return 0; } 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; }