X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_tview.c;h=7b326fc40e7bf276b7adc3848c0667d5628a68ad;hb=961c3fe158b5a9777bc8c061425ca3cb15d8687c;hp=441a1b4c9581a628735713cfc1464e87c548ff95;hpb=030a404097c6f8b094eca03a8380b35ff81e6c70;p=samtools.git

diff --git a/bam_tview.c b/bam_tview.c
index 441a1b4..7b326fc 100644
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -52,7 +52,7 @@ typedef struct {
 	faidx_t *fai;
 	bam_maqcns_t *bmc;
 
-	int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins;
+	int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
 	char *ref;
 } tview_t;
 
@@ -100,20 +100,28 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 						c = bam_aux_getCSi(p->b, p->qpos);
 						// assume that if we found one color, we will be able to get the color error
 						if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
-					}
-					else {
-						c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
-						if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+					} else {
+						if (tv->show_name) {
+							char *name = bam1_qname(p->b);
+							c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
+						} else {
+							c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+							if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+						}
 					}
 				} else c = '*';
 			} else { // padding
 				if (j > p->indel) c = '*';
 				else { // insertion
 					if (tv->base_for ==  TV_BASE_NUCL) {
-						c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
-						if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
-					}
-					else {
+						if (tv->show_name) {
+							char *name = bam1_qname(p->b);
+							c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
+						} else {
+							c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+							if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+						}
+					} else {
 						c = bam_aux_getCSi(p->b, p->qpos + j);
 						if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.';
 					}
@@ -195,7 +203,7 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
 	tv->mrow = 24; tv->mcol = 80;
 	getmaxyx(stdscr, tv->mrow, tv->mcol);
 	tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
-	tv->whelp = newwin(27, 40, 5, 5);
+	tv->whelp = newwin(29, 40, 5, 5);
 	tv->color_for = TV_COLOR_MAPQ;
 	start_color();
 	init_pair(1, COLOR_BLUE, COLOR_BLACK);
@@ -228,6 +236,14 @@ void tv_destroy(tview_t *tv)
 int tv_fetch_func(const bam1_t *b, void *data)
 {
 	tview_t *tv = (tview_t*)data;
+	if (tv->no_skip) {
+		uint32_t *cigar = bam1_cigar(b); // this is cheating...
+		int i;
+		for (i = 0; i <b->core.n_cigar; ++i) {
+			if ((cigar[i]&0xf) == BAM_CREF_SKIP)
+				cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
+		}
+	}
 	bam_lplbuf_push(b, tv->lplbuf);
 	return 0;
 }
@@ -264,7 +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: ");
@@ -275,10 +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);
+				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;
@@ -311,6 +335,8 @@ static void tv_win_help(tview_t *tv) {
 	mvwprintw(win, r++, 2, "c          Color for cs color");
 	mvwprintw(win, r++, 2, "z          Color for cs qual");
 	mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
+	mvwprintw(win, r++, 2, "s          Toggle on/off ref skip");
+	mvwprintw(win, r++, 2, "r          Toggle on/off rd name");
 	mvwprintw(win, r++, 2, "N          Turn on nt view");
 	mvwprintw(win, r++, 2, "C          Turn on cs view");
 	mvwprintw(win, r++, 2, "i          Toggle on/off ins");
@@ -333,12 +359,15 @@ 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;
 			case 'n': tv->color_for = TV_COLOR_NUCL; break;
 			case 'c': tv->color_for = TV_COLOR_COL; break;
 			case 'z': tv->color_for = TV_COLOR_COLQ; break;
+			case 's': tv->no_skip = !tv->no_skip; break;
+			case 'r': tv->show_name = !tv->show_name; break;
 			case KEY_LEFT:
 			case 'h': --pos; break;
 			case KEY_RIGHT: