1 #include "bam_tview_curses.h"
6 static void curses_tv_destroy(tview_t* base)
8 curses_tview_t* tv=(curses_tview_t*)base;
11 delwin(tv->wgoto); delwin(tv->whelp);
14 base_tv_destroy(base);
19 curses_tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
21 curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
22 tview_t* base=(tview_t*)tv;
25 fprintf(stderr,"Calloc failed\n");
29 base_tv_init(base,fn,fn_fa,samples);
30 /* initialize callbacks */
31 base->destroy=curses_tv_destroy;
39 getmaxyx(stdscr, base->mrow, base->mcol);
40 tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
41 tv->whelp = newwin(29, 40, 5, 5);
44 init_pair(1, COLOR_BLUE, COLOR_BLACK);
45 init_pair(2, COLOR_GREEN, COLOR_BLACK);
46 init_pair(3, COLOR_YELLOW, COLOR_BLACK);
47 init_pair(4, COLOR_WHITE, COLOR_BLACK);
48 init_pair(5, COLOR_GREEN, COLOR_BLACK);
49 init_pair(6, COLOR_CYAN, COLOR_BLACK);
50 init_pair(7, COLOR_YELLOW, COLOR_BLACK);
51 init_pair(8, COLOR_RED, COLOR_BLACK);
52 init_pair(9, COLOR_BLUE, COLOR_BLACK);
57 static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
61 tview_t *base=(tview_t*)tv;
62 wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
63 mvwprintw(tv->wgoto, 1, 2, "Goto: ");
65 int c = wgetch(tv->wgoto);
67 if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
69 } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
70 int _tid = -1, _beg, _end;
72 _beg = strtol(str+1, &p, 10) - 1;
78 bam_parse_region(base->header, str, &_tid, &_beg, &_end);
80 *tid = _tid; *pos = _beg;
84 } else if (isgraph(c)) {
85 if (l < TV_MAX_GOTO) str[l++] = c;
86 } else if (c == '\027') l = 0;
87 else if (c == '\033') return;
89 for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
90 mvwprintw(tv->wgoto, 1, 8, "%s", str);
97 static void tv_win_help(curses_tview_t *tv) {
99 tview_t* base=(tview_t*)base;
100 WINDOW *win = tv->whelp;
101 wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
102 mvwprintw(win, r++, 2, " -=- Help -=- ");
104 mvwprintw(win, r++, 2, "? This window");
105 mvwprintw(win, r++, 2, "Arrows Small scroll movement");
106 mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
107 mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
108 mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
109 mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
110 mvwprintw(win, r++, 2, "space Scroll one screen");
111 mvwprintw(win, r++, 2, "backspace Scroll back one screen");
112 mvwprintw(win, r++, 2, "g Go to specific location");
113 mvwprintw(win, r++, 2, "m Color for mapping qual");
114 mvwprintw(win, r++, 2, "n Color for nucleotide");
115 mvwprintw(win, r++, 2, "b Color for base quality");
116 mvwprintw(win, r++, 2, "c Color for cs color");
117 mvwprintw(win, r++, 2, "z Color for cs qual");
118 mvwprintw(win, r++, 2, ". Toggle on/off dot view");
119 mvwprintw(win, r++, 2, "s Toggle on/off ref skip");
120 mvwprintw(win, r++, 2, "r Toggle on/off rd name");
121 mvwprintw(win, r++, 2, "N Turn on nt view");
122 mvwprintw(win, r++, 2, "C Turn on cs view");
123 mvwprintw(win, r++, 2, "i Toggle on/off ins");
124 mvwprintw(win, r++, 2, "q Exit");
126 mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
127 mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
128 mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
133 void tv_loop(curses_tview_t *CTV)
136 tview_t* tv=(tview_t*)CTV;
137 tid = tv->curr_tid; pos = tv->left_pos;
141 case '?': tv_win_help(CTV); break;
143 case 'q': goto end_loop;
145 case 'g': tv_win_goto(CTV, &tid, &pos); break;
146 case 'm': tv->color_for = TV_COLOR_MAPQ; break;
147 case 'b': tv->color_for = TV_COLOR_BASEQ; break;
148 case 'n': tv->color_for = TV_COLOR_NUCL; break;
149 case 'c': tv->color_for = TV_COLOR_COL; break;
150 case 'z': tv->color_for = TV_COLOR_COLQ; break;
151 case 's': tv->no_skip = !tv->no_skip; break;
152 case 'r': tv->show_name = !tv->show_name; break;
154 case 'h': --pos; break;
156 case 'l': ++pos; break;
158 case 'H': pos -= 20; break;
160 case 'L': pos += 20; break;
161 case '.': tv->is_dot = !tv->is_dot; break;
162 case 'N': tv->base_for = TV_BASE_NUCL; break;
163 case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
164 case 'i': tv->ins = !tv->ins; break;
165 case '\010': pos -= 1000; break;
166 case '\014': pos += 1000; break;
167 case ' ': pos += tv->mcol; break;
169 case 'j': --tv->row_shift; break;
171 case 'k': ++tv->row_shift; break;
173 case '\177': pos -= tv->mcol; break;
174 case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
177 if (pos < 0) pos = 0;
178 if (tv->row_shift < 0) tv->row_shift = 0;
179 tv_draw_aln(tv, tid, pos);
185 void error(const char *format, ...)
189 fprintf(stderr, "\n");
190 fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
191 fprintf(stderr, "Options:\n");
192 fprintf(stderr, " -p chr:pos go directly to this position\n");
193 fprintf(stderr, " -s STR display only reads from this sample or grou\n");
194 fprintf(stderr, "\n\n");
199 va_start(ap, format);
200 vfprintf(stderr, format, ap);
207 int bam_tview_main(int argc, char *argv[])
211 char *samples=NULL, *position=NULL;
213 while ((c = getopt(argc, argv, "s:p:")) >= 0) {
215 case 's': samples=optarg; break;
216 case 'p': position=optarg; break;
217 default: error(NULL);
220 if (argc==optind) error(NULL);
221 CTV = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
225 int _tid = -1, _beg, _end;
226 bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
227 if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
229 tv_draw_aln(tv, tv->curr_tid, tv->left_pos);