new file mode 100644

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+#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;

+}