* Merge from branches/dev/

[samtools.git] / bam_lpileup.c

diff --git a/bam_lpileup.c b/bam_lpileup.c
index 83f91c2d3edb39ffce3212ee1751e0fcec36d43f..368028766842db8b9b71c82c4fc85a2eb3a87092 100644 (file)
--- a/bam_lpileup.c
+++ b/bam_lpileup.c
@@ -92,7 +92,7 @@ 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;
@@ -146,7 +146,7 @@ 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;
@@ -180,13 +180,14 @@ 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)
+int bam_lpileup_file(bamFile fp, int mask, 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);
+       bam_plbuf_set_mask(buf->plbuf, mask);
        while ((ret = bam_read1(fp, b)) >= 0)
                bam_lplbuf_push(b, buf);
        bam_lplbuf_push(0, buf);