X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_tview.c;h=bf01e15c3d79b1a55920bd4162c8e347b9f1f0d7;hp=4c121e7cbfa012ac0c3fa61d574f03c893e6d271;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/bam_tview.c b/bam_tview.c
index 4c121e7..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();
@@ -280,7 +280,7 @@ int tv_draw_aln(tview_t *tv, int tid, int pos)
 
 static void tv_win_goto(tview_t *tv, int *tid, int *pos)
 {
-	char str[256];
+	char str[256], *p;
 	int i, l = 0;
 	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
 	mvwprintw(tv->wgoto, 1, 2, "Goto: ");
@@ -291,10 +291,18 @@ static void tv_win_goto(tview_t *tv, int *tid, int *pos)
 			--l;
 		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
 			int _tid = -1, _beg, _end;
-			bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
-			if (_tid >= 0) {
-				*tid = _tid; *pos = _beg;
-				return;
+			if (str[0] == '=') {
+				_beg = strtol(str+1, &p, 10) - 1;
+				if (_beg > 0) {
+					*pos = _beg;
+					return;
+				}
+			} else {
+				bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
+				if (_tid >= 0) {
+					*tid = _tid; *pos = _beg;
+					return;
+				}
 			}
 		} else if (isgraph(c)) {
 			if (l < TV_MAX_GOTO) str[l++] = c;
@@ -351,6 +359,7 @@ void tv_loop(tview_t *tv)
 			case '?': tv_win_help(tv); break;
 			case '\033':
 			case 'q': goto end_loop;
+			case '/': 
 			case 'g': tv_win_goto(tv, &tid, &pos); break;
 			case 'm': tv->color_for = TV_COLOR_MAPQ; break;
 			case 'b': tv->color_for = TV_COLOR_BASEQ; break;