diff pyPRADA_1.2/tools/samtools-0.1.16/bam_tview.c @ 0:acc2ca1a3ba4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/bam_tview.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,424 @@
+#undef _HAVE_CURSES
+
+#if _CURSES_LIB == 0
+#elif _CURSES_LIB == 1
+#include <curses.h>
+#ifndef NCURSES_VERSION
+#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
+#else
+#define _HAVE_CURSES
+#endif
+#elif _CURSES_LIB == 2
+#include <xcurses.h>
+#define _HAVE_CURSES
+#else
+#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
+#endif
+
+#ifdef _HAVE_CURSES
+#include <ctype.h>
+#include <assert.h>
+#include <string.h>
+#include "bam.h"
+#include "faidx.h"
+#include "bam_maqcns.h"
+
+char bam_aux_getCEi(bam1_t *b, int i);
+char bam_aux_getCSi(bam1_t *b, int i);
+char bam_aux_getCQi(bam1_t *b, int i);
+
+#define TV_MIN_ALNROW 2
+#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_COL    3
+#define TV_COLOR_COLQ   4
+
+#define TV_BASE_NUCL 0
+#define TV_BASE_COLOR_SPACE 1
+
+typedef struct {
+	int mrow, mcol;
+	WINDOW *wgoto, *whelp;
+
+	bam_index_t *idx;
+	bam_lplbuf_t *lplbuf;
+	bam_header_t *header;
+	bamFile fp;
+	int curr_tid, left_pos;
+	faidx_t *fai;
+	bam_maqcns_t *bmc;
+
+	int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
+	char *ref;
+} tview_t;
+
+int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
+{
+	tview_t *tv = (tview_t*)data;
+	int i, j, c, rb, attr, max_ins = 0;
+	uint32_t call = 0;
+	if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
+	// print referece
+	rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
+	for (i = tv->last_pos + 1; i < pos; ++i) {
+		if (i%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", i+1);
+		c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
+		mvaddch(1, tv->ccol++, c);
+	}
+	if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
+	// print consensus
+	call = bam_maqcns_call(n, pl, tv->bmc);
+	attr = A_UNDERLINE;
+	c = ",ACMGRSVTWYHKDBN"[call>>28&0xf];
+	i = (call>>8&0xff)/10+1;
+	if (i > 4) i = 4;
+	attr |= COLOR_PAIR(i);
+	if (c == toupper(rb)) c = '.';
+	attron(attr);
+	mvaddch(2, tv->ccol, c);
+	attroff(attr);
+	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) {
+		for (i = 0; i < n; ++i) {
+			const bam_pileup1_t *p = pl + i;
+			int row = TV_MIN_ALNROW + p->level - tv->row_shift;
+			if (j == 0) {
+				if (!p->is_del) {
+					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 {
+						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 = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
+			} else { // padding
+				if (j > p->indel) c = '*';
+				else { // insertion
+					if (tv->base_for ==  TV_BASE_NUCL) {
+						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)? ',' : '.';
+					}
+				}
+			}
+			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;
+				if (tv->color_for == TV_COLOR_BASEQ) {
+					x = bam1_qual(p->b)[p->qpos]/10 + 1;
+					if (x > 4) x = 4;
+					attr |= COLOR_PAIR(x);
+				} else if (tv->color_for == TV_COLOR_MAPQ) {
+					x = p->b->core.qual/10 + 1;
+					if (x > 4) x = 4;
+					attr |= COLOR_PAIR(x);
+				} 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));
+				attroff(attr);
+			}
+		}
+		c = j? '*' : rb;
+		if (c == '*') {
+			attr = COLOR_PAIR(8);
+			attron(attr);
+			mvaddch(1, tv->ccol++, c);
+			attroff(attr);
+		} else mvaddch(1, tv->ccol++, c);
+	}
+	tv->last_pos = pos;
+	return 0;
+}
+
+tview_t *tv_init(const char *fn, const char *fn_fa)
+{
+	tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
+	tv->is_dot = 1;
+	tv->fp = bam_open(fn, "r");
+	bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
+	assert(tv->fp);
+	tv->header = bam_header_read(tv->fp);
+	tv->idx = bam_index_load(fn);
+	if (tv->idx == 0) exit(1);
+	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();
+	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(29, 40, 5, 5);
+	tv->color_for = TV_COLOR_MAPQ;
+	start_color();
+	init_pair(1, COLOR_BLUE, COLOR_BLACK);
+	init_pair(2, COLOR_GREEN, COLOR_BLACK);
+	init_pair(3, COLOR_YELLOW, COLOR_BLACK);
+	init_pair(4, COLOR_WHITE, COLOR_BLACK);
+	init_pair(5, COLOR_GREEN, COLOR_BLACK);
+	init_pair(6, COLOR_CYAN, COLOR_BLACK);
+	init_pair(7, COLOR_YELLOW, COLOR_BLACK);
+	init_pair(8, COLOR_RED, COLOR_BLACK);
+	init_pair(9, COLOR_BLUE, COLOR_BLACK);
+	return tv;
+}
+
+void tv_destroy(tview_t *tv)
+{
+	delwin(tv->wgoto); delwin(tv->whelp);
+	endwin();
+
+	bam_lplbuf_destroy(tv->lplbuf);
+	bam_maqcns_destroy(tv->bmc);
+	bam_index_destroy(tv->idx);
+	if (tv->fai) fai_destroy(tv->fai);
+	free(tv->ref);
+	bam_header_destroy(tv->header);
+	bam_close(tv->fp);
+	free(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;
+}
+
+int tv_draw_aln(tview_t *tv, int tid, int pos)
+{
+	// reset
+	clear();
+	tv->curr_tid = tid; tv->left_pos = pos;
+	tv->last_pos = tv->left_pos - 1;
+	tv->ccol = 0;
+	// print ref and consensus
+	if (tv->fai) {
+		char *str;
+		if (tv->ref) free(tv->ref);
+		str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
+		sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
+		tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
+		free(str);
+	}
+	// draw aln
+	bam_lplbuf_reset(tv->lplbuf);
+	bam_fetch(tv->fp, tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol, tv, tv_fetch_func);
+	bam_lplbuf_push(0, tv->lplbuf);
+
+	while (tv->ccol < tv->mcol) {
+		int pos = tv->last_pos + 1;
+		if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
+		mvaddch(1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
+		++tv->last_pos;
+	}
+	return 0;
+}
+
+static void tv_win_goto(tview_t *tv, int *tid, int *pos)
+{
+	char str[256], *p;
+	int i, l = 0;
+	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
+	mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+	for (;;) {
+		int c = wgetch(tv->wgoto);
+		wrefresh(tv->wgoto);
+		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
+			--l;
+		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
+			int _tid = -1, _beg, _end;
+			if (str[0] == '=') {
+				_beg = strtol(str+1, &p, 10) - 1;
+				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;
+		} else if (c == '\027') l = 0;
+		else if (c == '\033') return;
+		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;
+	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, "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, "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");
+	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);
+}
+
+void tv_loop(tview_t *tv)
+{
+	int tid, pos;
+	tid = tv->curr_tid; pos = tv->left_pos;
+	while (1) {
+		int c = getch();
+		switch (c) {
+			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:
+			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;
+			case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+			default: continue;
+		}
+		if (pos < 0) pos = 0;
+		if (tv->row_shift < 0) tv->row_shift = 0;
+		tv_draw_aln(tv, tid, pos);
+	}
+end_loop:
+	return;
+}
+
+int bam_tview_main(int argc, char *argv[])
+{
+	tview_t *tv;
+	if (argc == 1) {
+		fprintf(stderr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
+		return 1;
+	}
+	tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
+	tv_draw_aln(tv, 0, 0);
+	tv_loop(tv);
+	tv_destroy(tv);
+	return 0;
+}
+#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");
+	return 1;
+}
+#endif // #ifdef _HAVE_CURSES