works

[samtools.git] / bam_lpileup.c

diff --git a/bam_lpileup.c b/bam_lpileup.c
index 83f91c2d3edb39ffce3212ee1751e0fcec36d43f..d4dd63b99b85dd4c5811758153a56757c908a52c 100644 (file)
--- a/bam_lpileup.c
+++ b/bam_lpileup.c
@@ -1,5 +1,6 @@
 #include <stdlib.h>
 #include <stdio.h>
+#include <assert.h>
 #include "bam.h"
 #include "ksort.h"
 
@@ -92,7 +93,7 @@ static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl
        max_level = 0;
        for (i = l = 0; i < n; ++i) {
                const bam_pileup1_t *p = pl + i;
-               if (p->qpos == 0) {
+               if (p->is_head) {
                        if (tv->head->next && tv->head->cnt == 0) { // then take a free slot
                                freenode_t *p = tv->head->next;
                                tv->cur_level[i] = tv->head->level;
@@ -102,7 +103,7 @@ static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl
                        } else tv->cur_level[i] = ++tv->max_level;
                } else {
                        tv->cur_level[i] = tv->pre_level[l++];
-                       if (p->qpos == p->b->core.l_qseq - 1) { // then return a free slot
+                       if (p->is_tail) { // then return a free slot
                                tv->tail->level = tv->cur_level[i];
                                tv->tail->next = mp_alloc(tv->mp);
                                tv->tail = tv->tail->next;
@@ -146,10 +147,20 @@ static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl
        // squeeze out terminated levels
        for (i = l = 0; i < n; ++i) {
                const bam_pileup1_t *p = pl + i;
-               if (p->qpos != p->b->core.l_qseq - 1)
+               if (!p->is_tail)
                        tv->pre_level[l++] = tv->pre_level[i];
        }
        tv->n_pre = l;
+/*
+       fprintf(stderr, "%d\t", pos+1);
+       for (i = 0; i < n; ++i) {
+               const bam_pileup1_t *p = pl + i;
+               if (p->is_head) fprintf(stderr, "^");
+               if (p->is_tail) fprintf(stderr, "$");
+               fprintf(stderr, "%d,", p->level);
+       }
+       fprintf(stderr, "\n");
+*/
        return 0;
 }
 
@@ -167,11 +178,17 @@ bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data)
 
 void bam_lplbuf_destroy(bam_lplbuf_t *tv)
 {
-       mp_free(tv->mp, tv->head);
-       mp_destroy(tv->mp);
+       freenode_t *p, *q;
        free(tv->cur_level); free(tv->pre_level);
        bam_plbuf_destroy(tv->plbuf);
        free(tv->aux);
+       for (p = tv->head; p->next;) {
+               q = p->next;
+               mp_free(tv->mp, p); p = q;
+       }
+       mp_free(tv->mp, p);
+       assert(tv->mp->cnt == 0);
+       mp_destroy(tv->mp);
        free(tv);
 }
 
@@ -179,18 +196,3 @@ int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
 {
        return bam_plbuf_push(b, tv->plbuf);
 }
-
-int bam_lpileup_file(bamFile fp, bam_pileup_f func, void *func_data)
-{
-       bam_lplbuf_t *buf;
-       int ret;
-       bam1_t *b;
-       b = (bam1_t*)calloc(1, sizeof(bam1_t));
-       buf = bam_lplbuf_init(func, func_data);
-       while ((ret = bam_read1(fp, b)) >= 0)
-               bam_lplbuf_push(b, buf);
-       bam_lplbuf_push(0, buf);
-       bam_lplbuf_destroy(buf);
-       free(b->data); free(b);
-       return 0;
-}