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);
20 void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
21 void (*my_)(struct AbstractTview*,int,int,int);
22 void (*my_attron)(struct AbstractTview*,int);
23 void (*my_attroff)(struct AbstractTview*,int);
24 void (*my_clear)(struct AbstractTview*);
25 int (*my_colorpair)(struct AbstractTview*,int);
28 static void curses_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
31 static void curses_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
34 static void curses_attron(struct AbstractTview* tv,int flag)
37 static void curses_attroff(struct AbstractTview* tv,int flag)
40 static void curses_clear(struct AbstractTview* tv)
44 static int curses_colorpair(struct AbstractTview* tv,int flag)
49 #define SET_CALLBACK(fun) base->my_##fun=curses_##fun;
53 curses_tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
55 curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
56 tview_t* base=(tview_t*)tv;
59 fprintf(stderr,"Calloc failed\n");
63 base_tv_init(base,fn,fn_fa,samples);
64 /* initialize callbacks */
65 SET_CALLBACK(destroy);
66 SET_CALLBACK(mvprintw);
67 SET_CALLBACK(mvaddch);
69 SET_CALLBACK(attroff);
71 SET_CALLBACK(colorpair);
79 getmaxyx(stdscr, base->mrow, base->mcol);
80 tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
81 tv->whelp = newwin(29, 40, 5, 5);
84 init_pair(1, COLOR_BLUE, COLOR_BLACK);
85 init_pair(2, COLOR_GREEN, COLOR_BLACK);
86 init_pair(3, COLOR_YELLOW, COLOR_BLACK);
87 init_pair(4, COLOR_WHITE, COLOR_BLACK);
88 init_pair(5, COLOR_GREEN, COLOR_BLACK);
89 init_pair(6, COLOR_CYAN, COLOR_BLACK);
90 init_pair(7, COLOR_YELLOW, COLOR_BLACK);
91 init_pair(8, COLOR_RED, COLOR_BLACK);
92 init_pair(9, COLOR_BLUE, COLOR_BLACK);
97 static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
101 tview_t *base=(tview_t*)tv;
102 wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
103 mvwprintw(tv->wgoto, 1, 2, "Goto: ");
105 int c = wgetch(tv->wgoto);
107 if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
109 } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
110 int _tid = -1, _beg, _end;
112 _beg = strtol(str+1, &p, 10) - 1;
118 bam_parse_region(base->header, str, &_tid, &_beg, &_end);
120 *tid = _tid; *pos = _beg;
124 } else if (isgraph(c)) {
125 if (l < TV_MAX_GOTO) str[l++] = c;
126 } else if (c == '\027') l = 0;
127 else if (c == '\033') return;
129 for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
130 mvwprintw(tv->wgoto, 1, 8, "%s", str);
137 static void tv_win_help(curses_tview_t *tv) {
139 tview_t* base=(tview_t*)base;
140 WINDOW *win = tv->whelp;
141 wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
142 mvwprintw(win, r++, 2, " -=- Help -=- ");
144 mvwprintw(win, r++, 2, "? This window");
145 mvwprintw(win, r++, 2, "Arrows Small scroll movement");
146 mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
147 mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
148 mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
149 mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
150 mvwprintw(win, r++, 2, "space Scroll one screen");
151 mvwprintw(win, r++, 2, "backspace Scroll back one screen");
152 mvwprintw(win, r++, 2, "g Go to specific location");
153 mvwprintw(win, r++, 2, "m Color for mapping qual");
154 mvwprintw(win, r++, 2, "n Color for nucleotide");
155 mvwprintw(win, r++, 2, "b Color for base quality");
156 mvwprintw(win, r++, 2, "c Color for cs color");
157 mvwprintw(win, r++, 2, "z Color for cs qual");
158 mvwprintw(win, r++, 2, ". Toggle on/off dot view");
159 mvwprintw(win, r++, 2, "s Toggle on/off ref skip");
160 mvwprintw(win, r++, 2, "r Toggle on/off rd name");
161 mvwprintw(win, r++, 2, "N Turn on nt view");
162 mvwprintw(win, r++, 2, "C Turn on cs view");
163 mvwprintw(win, r++, 2, "i Toggle on/off ins");
164 mvwprintw(win, r++, 2, "q Exit");
166 mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
167 mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
168 mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
173 void tv_loop(curses_tview_t *CTV)
176 tview_t* tv=(tview_t*)CTV;
177 tid = tv->curr_tid; pos = tv->left_pos;
181 case '?': tv_win_help(CTV); break;
183 case 'q': goto end_loop;
185 case 'g': tv_win_goto(CTV, &tid, &pos); break;
186 case 'm': tv->color_for = TV_COLOR_MAPQ; break;
187 case 'b': tv->color_for = TV_COLOR_BASEQ; break;
188 case 'n': tv->color_for = TV_COLOR_NUCL; break;
189 case 'c': tv->color_for = TV_COLOR_COL; break;
190 case 'z': tv->color_for = TV_COLOR_COLQ; break;
191 case 's': tv->no_skip = !tv->no_skip; break;
192 case 'r': tv->show_name = !tv->show_name; break;
194 case 'h': --pos; break;
196 case 'l': ++pos; break;
198 case 'H': pos -= 20; break;
200 case 'L': pos += 20; break;
201 case '.': tv->is_dot = !tv->is_dot; break;
202 case 'N': tv->base_for = TV_BASE_NUCL; break;
203 case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
204 case 'i': tv->ins = !tv->ins; break;
205 case '\010': pos -= 1000; break;
206 case '\014': pos += 1000; break;
207 case ' ': pos += tv->mcol; break;
209 case 'j': --tv->row_shift; break;
211 case 'k': ++tv->row_shift; break;
213 case '\177': pos -= tv->mcol; break;
214 case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
217 if (pos < 0) pos = 0;
218 if (tv->row_shift < 0) tv->row_shift = 0;
219 tv_draw_aln(tv, tid, pos);
225 void error(const char *format, ...)
229 fprintf(stderr, "\n");
230 fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
231 fprintf(stderr, "Options:\n");
232 fprintf(stderr, " -p chr:pos go directly to this position\n");
233 fprintf(stderr, " -s STR display only reads from this sample or grou\n");
234 fprintf(stderr, "\n\n");
239 va_start(ap, format);
240 vfprintf(stderr, format, ap);
247 int bam_tview_main(int argc, char *argv[])
251 char *samples=NULL, *position=NULL;
253 while ((c = getopt(argc, argv, "s:p:")) >= 0) {
255 case 's': samples=optarg; break;
256 case 'p': position=optarg; break;
257 default: error(NULL);
260 if (argc==optind) error(NULL);
261 CTV = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
265 int _tid = -1, _beg, _end;
266 bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
267 if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
269 tv_draw_aln(tv, tv->curr_tid, tv->left_pos);