* samtools-0.1.5-23 (r434)

 * in tview, press 'r' to show read names rather than sequences

diff --git a/bam_tview.c b/bam_tview.c
index 019e3773cea2730a46d21277fe577b10f284a26b..4c121e7cbfa012ac0c3fa61d574f03c893e6d271 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, no_skip;
+       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(28, 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);
@@ -320,6 +328,7 @@ static void tv_win_help(tview_t *tv) {
        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");
@@ -349,6 +358,7 @@ void tv_loop(tview_t *tv)
                        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:

diff --git a/bamtk.c b/bamtk.c
index 6187e3241c6547297767b6cce0f7ba5d21999afe..7c6b5ffe06915e6b8bbeb645757627fe2c4593ff 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-22 (r432)"
+#define PACKAGE_VERSION "0.1.5-23 (r434)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);