* make tview more friendly

[samtools.git] / bam_tview.c

diff --git a/bam_tview.c b/bam_tview.c
index 2442994d3708912daf0823c1114eb0368d6961de..7b326fc40e7bf276b7adc3848c0667d5628a68ad 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, 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)? ',' : '.';
                                        }
@@ -192,13 +200,10 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
        clear();
        noecho();
        cbreak();
-#ifdef NCURSES_VERSION
+       tv->mrow = 24; tv->mcol = 80;
        getmaxyx(stdscr, tv->mrow, tv->mcol);
-#else
-       tv->mrow = 80; tv->mcol = 40;
-#endif
        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);
@@ -231,6 +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;
 }
@@ -267,7 +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: ");
@@ -278,10 +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;
@@ -314,6 +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");
@@ -336,12 +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:
@@ -387,8 +413,9 @@ int bam_tview_main(int argc, char *argv[])
        tv_destroy(tv);
        return 0;
 }
-#else // #ifdef NCURSES_VERSION
-#warning "The ncurses library is unavailable; tview is disabled."
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; tview is disabled."
 int bam_tview_main(int argc, char *argv[])
 {
        fprintf(stderr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");