X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_pileup.c;h=57434e098e2398fc4a6eab32b0d507d7724aa96e;hp=f68f400ab5cd086dc88a33e14899abe6cd4e53bb;hb=HEAD;hpb=d363084f0412f3bcdeb0304aeb0974c9a10c7649

diff --git a/bam_pileup.c b/bam_pileup.c
index f68f400..57434e0 100644
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -4,9 +4,16 @@
 #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;
 
@@ -53,174 +60,260 @@ static inline void mp_free(mempool_t *mp, lbnode_t *p)
 
 /* --- BEGIN: Auxiliary functions */
 
-static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
+/* 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)
 {
-	unsigned k;
+#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 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
+	uint32_t *cigar = bam1_cigar(b);
+	int k, is_head = 0;
+	// 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
+		is_head = 1;
+		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;
+				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 >= 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;
 			}
-			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);
+			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;
 			}
-			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;
 		}
+		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);
 	}
-	assert(x > pos); // otherwise a bug
-	return ret;
+	return 1;
 }
 
 /* --- END: Auxiliary functions */
 
-struct __bam_plbuf_t {
+/*******************
+ * pileup iterator *
+ *******************/
+
+struct __bam_plp_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;
+	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;
 };
 
-void bam_plbuf_reset(bam_plbuf_t *buf)
+bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
 {
-	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;
+	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();
 	}
-	buf->head = buf->tail;
+	return iter;
 }
 
-void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
+void bam_plp_destroy(bam_plp_t iter)
 {
-	if (mask < 0) buf->flag_mask = BAM_DEF_MASK;
-	else buf->flag_mask = BAM_FUNMAP | mask;
+	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);
 }
 
-bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
+const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
 {
-	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);
+	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_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
+int bam_plp_push(bam_plp_t iter, const bam1_t *b)
 {
-	if (b) { // fill buffer
+	if (iter->error) return -1;
+	if (b) {
 		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) {
+		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 == buf->max_tid) && (buf->tail->beg < buf->max_pos)) {
+		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;
 		}
-		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;
+		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 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;
+	} 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.
 		}
-		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;
+		bam_plp_push(iter, 0);
+		if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+		return 0;
 	}
-	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;
@@ -236,3 +329,109 @@ int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
 	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;
+}