X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_tview.c;fp=samtools%2Fbam_tview.c;h=0000000000000000000000000000000000000000;hp=7b326fc40e7bf276b7adc3848c0667d5628a68ad;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/samtools/bam_tview.c b/samtools/bam_tview.c
deleted file mode 100644
index 7b326fc..0000000
--- a/samtools/bam_tview.c
+++ /dev/null
@@ -1,424 +0,0 @@
-#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 = '*';
-			} 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->idx = bam_index_load(fn);
-	if (tv->idx == 0) exit(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->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);
-				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