X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_tview.c;h=bf01e15c3d79b1a55920bd4162c8e347b9f1f0d7;hp=7b326fc40e7bf276b7adc3848c0667d5628a68ad;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=67801bf17aa6495879da63ce77a2014759fabc16

diff --git a/bam_tview.c b/bam_tview.c
index 7b326fc..bf01e15 100644
--- 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();
@@ -292,7 +292,7 @@ static void tv_win_goto(tview_t *tv, int *tid, int *pos)
 		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
 			int _tid = -1, _beg, _end;
 			if (str[0] == '=') {
-				_beg = strtol(str+1, &p, 10);
+				_beg = strtol(str+1, &p, 10) - 1;
 				if (_beg > 0) {
 					*pos = _beg;
 					return;