* samtools-0.1.5-18 (r423)

[samtools.git] / bam_tview.c

diff --git a/bam_tview.c b/bam_tview.c
index 441a1b4c9581a628735713cfc1464e87c548ff95..019e3773cea2730a46d21277fe577b10f284a26b 100644 (file)
--- 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;
        char *ref;
 } tview_t;
 
@@ -195,7 +195,7 @@ 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(28, 40, 5, 5);
        tv->color_for = TV_COLOR_MAPQ;
        start_color();
        init_pair(1, COLOR_BLUE, COLOR_BLACK);
@@ -228,6 +228,14 @@ 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;
 }
@@ -311,6 +319,7 @@ 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, "N          Turn on nt view");
        mvwprintw(win, r++, 2, "C          Turn on cs view");
        mvwprintw(win, r++, 2, "i          Toggle on/off ins");
@@ -339,6 +348,7 @@ void tv_loop(tview_t *tv)
                        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 KEY_LEFT:
                        case 'h': --pos; break;
                        case KEY_RIGHT: