src/samtools/bam_pileup.c
5bb21ad5
 #include <stdio.h>
 #include <stdlib.h>
 #include <ctype.h>
 #include <assert.h>
 #include "sam.h"
 
 typedef struct {
 	int k, x, y, end;
 } cstate_t;
 
 static cstate_t g_cstate_null = { -1, 0, 0, 0 };
 
 typedef struct __linkbuf_t {
 	bam1_t b;
 	uint32_t beg, end;
 	cstate_t s;
 	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 */
 
 /* s->k: the index of the CIGAR operator that has just been processed.
    s->x: the reference coordinate of the start of s->k
    s->y: the query coordiante of the start of s->k
  */
 static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
 {
 #define _cop(c) ((c)&BAM_CIGAR_MASK)
 #define _cln(c) ((c)>>BAM_CIGAR_SHIFT)
 
 	bam1_t *b = p->b;
 	bam1_core_t *c = &b->core;
 	uint32_t *cigar = bam1_cigar(b);
 	int k;
 	// determine the current CIGAR operation
 //	fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam1_qname(b), pos, s->end, s->k, s->x, s->y);
 	if (s->k == -1) { // never processed
 		if (c->n_cigar == 1) { // just one operation, save a loop
 		  if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
 		} else { // find the first match or deletion
 			for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
 				int op = _cop(cigar[k]);
 				int l = _cln(cigar[k]);
 				if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break;
 				else if (op == BAM_CREF_SKIP) { s->x += l; break; }
 				else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
 			}
 			assert(k < c->n_cigar);
 			s->k = k;
 		}
 	} else { // the read has been processed before
 		int op, l = _cln(cigar[s->k]);
 		if ((pos >= s->x) && (pos - s->x >= l)) { // jump to the next operation
 			assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
 			op = _cop(cigar[s->k+1]);
 			if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop
 			  if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
 				s->x += l;
 				++s->k;
 			} else { // find the next M/D/N/=/X
 			  if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
 				s->x += l;
 				for (k = s->k + 1; k < c->n_cigar; ++k) {
 					op = _cop(cigar[k]), l = _cln(cigar[k]);
 					if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break;
 					else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
 				}
 				s->k = k;
 			}
 			assert(s->k < c->n_cigar); // otherwise a bug
 		} // else, do nothing
 	}
 	{ // collect pileup information
 		int op, l;
 		op = _cop(cigar[s->k]); l = _cln(cigar[s->k]);
 		p->is_del = p->indel = p->is_refskip = 0;
 		if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
 			int op2 = _cop(cigar[s->k+1]);
 			int l2 = _cln(cigar[s->k+1]);
 			if (op2 == BAM_CDEL) p->indel = -(int)l2;
 			else if (op2 == BAM_CINS) p->indel = l2;
 			else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
 				int l3 = 0;
 				for (k = s->k + 2; k < c->n_cigar; ++k) {
 					op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
 					if (op2 == BAM_CINS) l3 += l2;
 					else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break;
 				}
 				if (l3 > 0) p->indel = l3;
 			}
 		}
 		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
 			p->qpos = s->y + (pos - s->x);
 		} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
 			p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
 			p->is_refskip = (op == BAM_CREF_SKIP);
 		} // cannot be other operations; otherwise a bug
 		p->is_head = (pos == c->pos); p->is_tail = (pos == s->end);
 	}
 	return 1;
 }
 
 /* --- 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, maxcnt;
 	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;
 	iter->maxcnt = 8000;
 	if (func) {
 		iter->func = func;
 		iter->data = data;
 		iter->b = bam_init1();
 	}
 	return iter;
 }
 
 void bam_plp_destroy(bam_plp_t iter)
 {
 	bam_plp_reset(iter);        /* MTM */
 	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_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
 			}
 		}
 		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;
 		if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) return 0;
 		bam_copy1(&iter->tail->b, b);
 		iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
 		iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
 		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 { // no pileup line can be obtained; read alignments
 		*_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;
 			// otherwise no pileup line can be returned; read the next alignment.
 		}
 		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);
 }
 
 void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
 {
 	iter->maxcnt = maxcnt;
 }
 
 /*****************
  * 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_set_maxcnt(bam_mplp_t iter, int maxcnt)
 {
 	int i;
 	for (i = 0; i < iter->n; ++i)
 		iter->iter[i]->maxcnt = maxcnt;
 }
 
 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) { // FIXME: valgrind reports "uninitialised value(s) at this line"
 			n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
 			++ret;
 		} else n_plp[i] = 0, plp[i] = 0;
 	}
 	return ret;
 }