#define TV_MAX_GOTO 40
#define TV_LOW_MAPQ 10
-#define TV_COLOR_MAPQ 0
-#define TV_COLOR_BASEQ 1
-#define TV_COLOR_NUCL 2
+#define TV_COLOR_MAPQ 0
+#define TV_COLOR_BASEQ 1
+#define TV_COLOR_NUCL 2
+#define TV_COLOR_COL 3
+#define TV_COLOR_COLQ 4
+
+#define TV_BASE_NUCL 0
+#define TV_BASE_COLOR_SPACE 1
typedef struct {
int mrow, mcol;
faidx_t *fai;
bam_maqcns_t *bmc;
- int ccol, last_pos, row_shift, color_for, is_nucl, l_ref;
+ int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins;
char *ref;
} tview_t;
attron(attr);
mvaddch(2, tv->ccol, c);
attroff(attr);
- // calculate maximum insert
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pl + i;
- if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
+ if(tv->ins) {
+ // calculate maximum insert
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
+ }
}
// core loop
for (j = 0; j <= max_ins; ++j) {
int row = TV_MIN_ALNROW + p->level - tv->row_shift;
if (j == 0) {
if (!p->is_del) {
- c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
- if (!tv->is_nucl && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ if (tv->base_for == TV_BASE_COLOR_SPACE &&
+ (c = bam_aux_getCSi(p->b, p->qpos))) {
+ 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 c = '*';
} else { // padding
if (j > p->indel) c = '*';
else { // insertion
- c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
- if (j == 0 && !tv->is_nucl && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ 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 {
+ 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)? ',' : '.';
+ }
}
}
if (row > TV_MIN_ALNROW && row < tv->mrow) {
int x;
attr = 0;
if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
- || (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
+ || (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
if (tv->color_for == TV_COLOR_BASEQ) {
x = bam1_qual(p->b)[p->qpos]/10 + 1;
if (x > 4) x = 4;
} else if (tv->color_for == TV_COLOR_NUCL) {
x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
attr |= COLOR_PAIR(x);
+ } else if(tv->color_for == TV_COLOR_COL) {
+ x = 0;
+ switch(bam_aux_getCSi(p->b, p->qpos)) {
+ case '0': x = 0; break;
+ case '1': x = 1; break;
+ case '2': x = 2; break;
+ case '3': x = 3; break;
+ case '4': x = 4; break;
+ default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
+ }
+ x+=5;
+ attr |= COLOR_PAIR(x);
+ } else if(tv->color_for == TV_COLOR_COLQ) {
+ x = bam_aux_getCQi(p->b, p->qpos);
+ if(0 == x) x = bam1_qual(p->b)[p->qpos];
+ x = x/10 + 1;
+ if (x > 4) x = 4;
+ attr |= COLOR_PAIR(x);
}
attron(attr);
mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
if (fn_fa) tv->fai = fai_load(fn_fa);
tv->bmc = bam_maqcns_init();
+ tv->ins = 1;
bam_maqcns_prepare(tv->bmc);
initscr();
keypad(stdscr, TRUE);
- clear();
- noecho();
- cbreak();
+ clear();
+ noecho();
+ cbreak();
#ifdef NCURSES_VERSION
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(22,40, 5, 5);
+ tv->whelp = newwin(27, 40, 5, 5);
tv->color_for = TV_COLOR_MAPQ;
start_color();
init_pair(1, COLOR_BLUE, COLOR_BLACK);
char str[256];
int i, l = 0;
wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
- mvwprintw(tv->wgoto, 1, 2, "Goto: ");
- for (;;) {
+ mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+ for (;;) {
int c = wgetch(tv->wgoto);
wrefresh(tv->wgoto);
if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
str[l] = '\0';
for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
mvwprintw(tv->wgoto, 1, 8, "%s", str);
- }
+ }
}
static void tv_win_help(tview_t *tv) {
- int r = 1;
+ int r = 1;
WINDOW *win = tv->whelp;
- wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
- mvwprintw(win, r++, 2, " -=- Help -=- ");
- r++;
- mvwprintw(win, r++, 2, "? This window");
- mvwprintw(win, r++, 2, "Arrows Small scroll movement");
- mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
- mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
- mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
- mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
- mvwprintw(win, r++, 2, "space Scroll one screen");
- mvwprintw(win, r++, 2, "backspace Scroll back one screen");
- mvwprintw(win, r++, 2, "g Go to specific location");
- mvwprintw(win, r++, 2, "b Color for base quality");
- mvwprintw(win, r++, 2, "m Color for mapping qual");
- mvwprintw(win, r++, 2, "n Color for nucleotide");
- mvwprintw(win, r++, 2, ". Toggle on/off dot view");
- mvwprintw(win, r++, 2, "q Exit");
+ wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
+ mvwprintw(win, r++, 2, " -=- Help -=- ");
+ r++;
+ mvwprintw(win, r++, 2, "? This window");
+ mvwprintw(win, r++, 2, "Arrows Small scroll movement");
+ mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
+ mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
+ mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
+ mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
+ mvwprintw(win, r++, 2, "space Scroll one screen");
+ mvwprintw(win, r++, 2, "backspace Scroll back one screen");
+ mvwprintw(win, r++, 2, "g Go to specific location");
+ mvwprintw(win, r++, 2, "m Color for mapping qual");
+ mvwprintw(win, r++, 2, "n Color for nucleotide");
+ mvwprintw(win, r++, 2, "b Color for base quality");
+ 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, "N Turn on nt view");
+ mvwprintw(win, r++, 2, "C Turn on cs view");
+ mvwprintw(win, r++, 2, "i Toggle on/off ins");
+ mvwprintw(win, r++, 2, "q Exit");
r++;
mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
- wrefresh(win);
- wgetch(win);
+ wrefresh(win);
+ wgetch(win);
}
void tv_loop(tview_t *tv)
int c = getch();
if(256 < c) {c = 1 + (c%256);} // Terminal was displaying ctrl-H as 263 via ssh from Mac OS X 10.5 computer
switch (c) {
- case '?': tv_win_help(tv); break;
- case '\033':
- case 'q': goto end_loop;
- case 'g': tv_win_goto(tv, &tid, &pos); break;
- case 'b': tv->color_for = TV_COLOR_BASEQ; break;
- case 'm': tv->color_for = TV_COLOR_MAPQ; break;
- case 'n': tv->color_for = TV_COLOR_NUCL; break;
- case KEY_LEFT:
- case 'h': --pos; break;
- case KEY_RIGHT:
- case 'l': ++pos; break;
- case KEY_SLEFT:
- case 'H': pos -= 20; break;
- case KEY_SRIGHT:
- case 'L': pos += 20; break;
- case '.': tv->is_nucl = !tv->is_nucl; break;
- case '\010': pos -= 1000; break;
- case '\014': pos += 1000; break;
- case ' ': pos += tv->mcol; break;
- case KEY_UP:
- case 'j': --tv->row_shift; break;
- case KEY_DOWN:
- case 'k': ++tv->row_shift; break;
- case KEY_BACKSPACE:
- case '\177': pos -= tv->mcol; break;
+ case '?': tv_win_help(tv); break;
+ case '\033':
+ case 'q': goto end_loop;
+ 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 KEY_LEFT:
+ case 'h': --pos; break;
+ case KEY_RIGHT:
+ case 'l': ++pos; break;
+ case KEY_SLEFT:
+ case 'H': pos -= 20; break;
+ case KEY_SRIGHT:
+ case 'L': pos += 20; break;
+ case '.': tv->is_dot = !tv->is_dot; break;
+ case 'N': tv->base_for = TV_BASE_NUCL; break;
+ case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
+ case 'i': tv->ins = !tv->ins; break;
+ case '\010': pos -= 1000; break;
+ case '\014': pos += 1000; break;
+ case ' ': pos += tv->mcol; break;
+ case KEY_UP:
+ case 'j': --tv->row_shift; break;
+ case KEY_DOWN:
+ case 'k': ++tv->row_shift; break;
+ case KEY_BACKSPACE:
+ case '\177': pos -= tv->mcol; break;
#ifdef KEY_RESIZE
- case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+ case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
#endif
- default: continue;
+ default: continue;
}
if (pos < 0) pos = 0;
if (tv->row_shift < 0) tv->row_shift = 0;
projects / samtools.git / blobdiff