* Added Brent's method for frequency estimate

[samtools.git] / bam_tview.c

diff --git a/bam_tview.c b/bam_tview.c
index 24cd12a5bf743dba2948ee92bd9c5c490c30e4ce..bf01e15c3d79b1a55920bd4162c8e347b9f1f0d7 100644 (file)
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -109,7 +109,7 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
                                                        if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
                                                }
                                        }
-                               } else c = '*';
+                               } else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
                        } else { // padding
                                if (j > p->indel) c = '*';
                                else { // insertion
@@ -183,12 +183,12 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
 {
        tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
        tv->is_dot = 1;
-       tv->idx = bam_index_load(fn);
-       if (tv->idx == 0) exit(1);
        tv->fp = bam_open(fn, "r");
        bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
        assert(tv->fp);
        tv->header = bam_header_read(tv->fp);
+       tv->idx = bam_index_load(fn);
+       if (tv->idx == 0) exit(1);
        tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
        if (fn_fa) tv->fai = fai_load(fn_fa);
        tv->bmc = bam_maqcns_init();