X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_pileup.c;fp=samtools%2Fbam_pileup.c;h=0000000000000000000000000000000000000000;hp=3c41a169127fcc5d3977df3e8febd944b7ced77e;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/samtools/bam_pileup.c b/samtools/bam_pileup.c
deleted file mode 100644
index 3c41a16..0000000
--- a/samtools/bam_pileup.c
+++ /dev/null
@@ -1,396 +0,0 @@
-#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;
-}