AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
- cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o
+ cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
+ bam_tview_curses.o bam_tview_html.o
PROG= samtools
INCLUDES= -I.
SUBDIRS= . bcftools misc
$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
razip:razip.o razf.o $(KNETFILE_O)
- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
+ $(CC) $(CFLAGS) -o $@ $^ -lz
bgzip:bgzip.o bgzf.o $(KNETFILE_O)
- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz -lpthread
+ $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
bgzf.o:bgzf.c bgzf.h
$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
bam_lpileup.o:bam.h ksort.h
-bam_tview.o:bam.h faidx.h
+bam_tview.o:bam.h faidx.h bam_tview.h
+bam_tview_curses.o:bam.h faidx.h bam_tview.h
+bam_tview_html.o:bam.h faidx.h bam_tview.h
bam_sort.o:bam.h ksort.h razf.h
bam_md.o:bam.h faidx.h
sam_header.o:sam_header.h khash.h
-#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 <math.h>
-#include <unistd.h>
-#include "bam.h"
-#include "faidx.h"
-#include "bam2bcf.h"
-#include "sam_header.h"
-#include "khash.h"
-
-KHASH_MAP_INIT_STR(kh_rg, const char *)
+#include "bam_tview.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
+int base_tv_init(tview_t* tv,const char *fn, const char *fn_fa, const char *samples)
+ {
+ assert(tv!=NULL);
+ assert(fn!=NULL);
+ tv->mrow = 24; tv->mcol = 80;
+ tv->color_for = TV_COLOR_MAPQ;
+ tv->is_dot = 1;
+
+ tv->fp = bam_open(fn, "r");
+ if(tv->fp==0)
+ {
+ fprintf(stderr,"bam_open %s. %s\n", fn,fn_fa);
+ exit(EXIT_FAILURE);
+ }
+ bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
+ assert(tv->fp);
+
+ tv->header = bam_header_read(tv->fp);
+ if(tv->header==0)
+ {
+ fprintf(stderr,"Cannot read '%s'.\n", fn);
+ exit(EXIT_FAILURE);
+ }
+ tv->idx = bam_index_load(fn);
+ if (tv->idx == 0)
+ {
+ fprintf(stderr,"Cannot read index for '%s'.\n", fn);
+ exit(EXIT_FAILURE);
+ }
+ tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
+ if (fn_fa) tv->fai = fai_load(fn_fa);
+ tv->bca = bcf_call_init(0.83, 13);
+ tv->ins = 1;
-#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
+ if ( samples )
+ {
+ if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text);
+ void *iter = tv->header->dict;
+ const char *key, *val;
+ int n = 0;
+ tv->rg_hash = kh_init(kh_rg);
+ while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) )
+ {
+ if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) )
+ {
+ khiter_t k = kh_get(kh_rg, tv->rg_hash, key);
+ if ( k != kh_end(tv->rg_hash) ) continue;
+ int ret;
+ k = kh_put(kh_rg, tv->rg_hash, key, &ret);
+ kh_value(tv->rg_hash, k) = val;
+ n++;
+ }
+ }
+ if ( !n )
+ {
+ fprintf(stderr,"The sample or read group \"%s\" not present.\n", samples);
+ exit(EXIT_FAILURE);
+ }
+ }
-#define TV_BASE_NUCL 0
-#define TV_BASE_COLOR_SPACE 1
+ return 0;
+ }
-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;
- bcf_callaux_t *bca;
+void base_tv_destroy(tview_t* tv)
+ {
+ bam_lplbuf_destroy(tv->lplbuf);
+ bcf_call_destroy(tv->bca);
+ bam_index_destroy(tv->idx);
+ if (tv->fai) fai_destroy(tv->fai);
+ free(tv->ref);
+ bam_header_destroy(tv->header);
+ bam_close(tv->fp);
+ }
- int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
- char *ref;
- khash_t(kh_rg) *rg_hash;
-} tview_t;
int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
// 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);
+ if (i%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1);
c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
- mvaddch(1, tv->ccol++, c);
+ tv->my_mvaddch(tv,1, tv->ccol++, c);
}
- if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
+ if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
{ // call consensus
bcf_callret1_t bcr;
int qsum[4], a1, a2, tmp;
else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
}
- attr = A_UNDERLINE;
+ attr = tv->my_underline(tv);
c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
i = (call&0xffff)/10+1;
if (i > 4) i = 4;
- attr |= COLOR_PAIR(i);
+ attr |= tv->my_colorpair(tv,i);
if (c == toupper(rb)) c = '.';
- attron(attr);
- mvaddch(2, tv->ccol, c);
- attroff(attr);
+ tv->my_attron(tv,attr);
+ tv->my_mvaddch(tv,2, tv->ccol, c);
+ tv->my_attroff(tv,attr);
if(tv->ins) {
// calculate maximum insert
for (i = 0; i < n; ++i) {
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 |= tv->my_underline(tv);
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);
+ attr |= tv->my_colorpair(tv,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);
+ attr |= tv->my_colorpair(tv,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);
+ attr |= tv->my_colorpair(tv,x);
} else if(tv->color_for == TV_COLOR_COL) {
x = 0;
switch(bam_aux_getCSi(p->b, p->qpos)) {
default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
}
x+=5;
- attr |= COLOR_PAIR(x);
+ attr |= tv->my_colorpair(tv,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);
+ attr |= tv->my_colorpair(tv,x);
}
- attron(attr);
- mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
- attroff(attr);
+ tv->my_attron(tv,attr);
+ tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
+ tv->my_attroff(tv,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);
+ attr = tv->my_colorpair(tv,8);
+ tv->my_attron(tv,attr);
+ tv->my_mvaddch(tv,1, tv->ccol++, c);
+ tv->my_attroff(tv,attr);
+ } else tv->my_mvaddch(tv,1, tv->ccol++, c);
}
tv->last_pos = pos;
return 0;
}
-tview_t *tv_init(const char *fn, const char *fn_fa, char *samples)
-{
- 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->bca = bcf_call_init(0.83, 13);
- tv->ins = 1;
- if ( samples )
- {
- if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text);
- void *iter = tv->header->dict;
- const char *key, *val;
- int n = 0;
- tv->rg_hash = kh_init(kh_rg);
- while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) )
- {
- if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) )
- {
- khiter_t k = kh_get(kh_rg, tv->rg_hash, key);
- if ( k != kh_end(tv->rg_hash) ) continue;
- int ret;
- k = kh_put(kh_rg, tv->rg_hash, key, &ret);
- kh_value(tv->rg_hash, k) = val;
- n++;
- }
- }
- if ( !n )
- {
- fprintf(stderr,"The sample or read group \"%s\" not present.\n", samples);
- exit(-1);
- }
- }
-
- 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);
- bcf_call_destroy(tv->bca);
- 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)
{
return 0;
}
-int tv_draw_aln(tview_t *tv, int tid, int pos)
-{
+int base_draw_aln(tview_t *tv, int tid, int pos)
+ {
+ assert(tv!=NULL);
// reset
- clear();
+ tv->my_clear(tv);
tv->curr_tid = tid; tv->left_pos = pos;
tv->last_pos = tv->left_pos - 1;
tv->ccol = 0;
if (tv->fai) {
char *str;
if (tv->ref) free(tv->ref);
+ assert(tv->curr_tid>=0);
+
str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
+ assert(str!=NULL);
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);
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');
+ if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
+ tv->my_mvaddch(tv,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') {
- if(l > 0) --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;
-}
-void error(const char *format, ...)
+static void error(const char *format, ...)
{
if ( !format )
{
fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -p chr:pos go directly to this position\n");
- fprintf(stderr, " -s STR display only reads from this sample or grou\n");
+ fprintf(stderr, " -s STR display only reads from this sample or group\n");
+ fprintf(stderr, " -d display (H)tml or (C)urses or (T)ext \n");
fprintf(stderr, "\n\n");
}
else
exit(-1);
}
+enum dipsay_mode {display_ncurses,display_html,display_text};
+extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
int bam_tview_main(int argc, char *argv[])
-{
- tview_t *tv;
+ {
+ int view_mode=display_ncurses;
+ tview_t* tv=NULL;
char *samples=NULL, *position=NULL;
int c;
- while ((c = getopt(argc, argv, "s:p:")) >= 0) {
+ while ((c = getopt(argc, argv, "s:p:d:")) >= 0) {
switch (c) {
case 's': samples=optarg; break;
case 'p': position=optarg; break;
+ case 'd':
+ {
+ switch(optarg[0])
+ {
+ case 'H': case 'h': view_mode=display_html;break;
+ case 'T': case 't': view_mode=display_text;break;
+ case 'C': case 'c': view_mode=display_ncurses;break;
+ default: view_mode=display_ncurses;break;
+ }
+ break;
+ }
default: error(NULL);
}
}
if (argc==optind) error(NULL);
- tv = tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
- if ( position )
- {
- int _tid = -1, _beg, _end;
- bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
- if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
- }
- tv_draw_aln(tv, tv->curr_tid, tv->left_pos);
- 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
+
+ switch(view_mode)
+ {
+ case display_ncurses:
+ {
+ tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+ break;
+ }
+ case display_text:
+ {
+ tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+ break;
+ }
+ case display_html:
+ {
+ tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+ break;
+ }
+ }
+ if(tv==NULL)
+ {
+ error("cannot create view");
+ return EXIT_FAILURE;
+ }
+
+ if ( position )
+ {
+ int _tid = -1, _beg, _end;
+ bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
+ if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
+ }
+ tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
+ tv->my_loop(tv);
+ tv->my_destroy(tv);
+
+ return EXIT_SUCCESS;
+ }
--- /dev/null
+#ifndef BAM_TVIEW_H
+#define BAM_TVIEW_H
+
+#include <ctype.h>
+#include <assert.h>
+#include <string.h>
+#include <math.h>
+#include <unistd.h>
+#include <stdarg.h>
+#include "bam.h"
+#include "faidx.h"
+#include "bam2bcf.h"
+#include "sam_header.h"
+#include "khash.h"
+
+KHASH_MAP_INIT_STR(kh_rg, const char *)
+
+typedef struct AbstractTview {
+ int mrow, mcol;
+
+ bam_index_t *idx;
+ bam_lplbuf_t *lplbuf;
+ bam_header_t *header;
+ bamFile fp;
+ int curr_tid, left_pos;
+ faidx_t *fai;
+ bcf_callaux_t *bca;
+
+ int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
+ char *ref;
+ khash_t(kh_rg) *rg_hash;
+ /* callbacks */
+ void (*my_destroy)(struct AbstractTview* );
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+ void (*my_mvaddch)(struct AbstractTview*,int,int,int);
+ void (*my_attron)(struct AbstractTview*,int);
+ void (*my_attroff)(struct AbstractTview*,int);
+ void (*my_clear)(struct AbstractTview*);
+ int (*my_colorpair)(struct AbstractTview*,int);
+ int (*my_drawaln)(struct AbstractTview*,int,int);
+ int (*my_loop)(struct AbstractTview*);
+ int (*my_underline)(struct AbstractTview*);
+} tview_t;
+
+
+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
+
+int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
+int base_tv_init(tview_t*,const char *fn, const char *fn_fa, const char *samples);
+void base_tv_destroy(tview_t*);
+int base_draw_aln(tview_t *tv, int tid, int pos);
+
+typedef struct Tixel
+ {
+ int ch;
+ int attributes;
+ }tixel_t;
+
+#endif
+
--- /dev/null
+#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
+
+
+#include "bam_tview.h"
+
+#ifdef _HAVE_CURSES
+
+
+
+typedef struct CursesTview {
+ tview_t view;
+ WINDOW *wgoto, *whelp;
+ } curses_tview_t;
+
+
+
+
+#define FROM_TV(ptr) ((curses_tview_t*)ptr)
+
+static void curses_destroy(tview_t* base)
+ {
+ curses_tview_t* tv=(curses_tview_t*)base;
+
+
+ delwin(tv->wgoto); delwin(tv->whelp);
+ endwin();
+
+ base_tv_destroy(base);
+
+ free(tv);
+ }
+
+/*
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+ void (*my_)(struct AbstractTview*,int,int,int);
+ void (*my_attron)(struct AbstractTview*,int);
+ void (*my_attroff)(struct AbstractTview*,int);
+ void (*my_clear)(struct AbstractTview*);
+ int (*my_colorpair)(struct AbstractTview*,int);
+*/
+
+static void curses_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
+ {
+ unsigned int size=tv->mcol+2;
+ char* str=malloc(size);
+ if(str==0) exit(EXIT_FAILURE);
+ va_list argptr;
+ va_start(argptr, fmt);
+ vsnprintf(str,size, fmt, argptr);
+ va_end(argptr);
+ mvprintw(y,x,str);
+ free(str);
+ }
+
+static void curses_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
+ {
+ mvaddch(y,x,ch);
+ }
+
+static void curses_attron(struct AbstractTview* tv,int flag)
+ {
+ attron(flag);
+ }
+static void curses_attroff(struct AbstractTview* tv,int flag)
+ {
+ attroff(flag);
+ }
+static void curses_clear(struct AbstractTview* tv)
+ {
+ clear();
+ }
+
+static int curses_colorpair(struct AbstractTview* tv,int flag)
+ {
+ return COLOR_PAIR(flag);
+ }
+
+static int curses_drawaln(struct AbstractTview* tv, int tid, int pos)
+ {
+ return base_draw_aln(tv, tid, pos);
+ }
+
+
+
+static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
+ {
+ char str[256], *p;
+ int i, l = 0;
+ tview_t *base=(tview_t*)tv;
+ 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') {
+ if(l > 0) --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(base->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(curses_tview_t *tv) {
+ int r = 1;
+ tview_t* base=(tview_t*)base;
+ 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);
+}
+
+static int curses_underline(tview_t* tv)
+ {
+ return A_UNDERLINE;
+ }
+
+static int curses_loop(tview_t* tv)
+ {
+ int tid, pos;
+ curses_tview_t *CTV=(curses_tview_t *)tv;
+ tid = tv->curr_tid; pos = tv->left_pos;
+ while (1) {
+ int c = getch();
+ switch (c) {
+ case '?': tv_win_help(CTV); break;
+ case '\033':
+ case 'q': goto end_loop;
+ case '/':
+ case 'g': tv_win_goto(CTV, &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->my_drawaln(tv, tid, pos);
+ }
+end_loop:
+ return 0;
+}
+
+
+
+
+tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
+ tview_t* base=(tview_t*)tv;
+ if(tv==0)
+ {
+ fprintf(stderr,"Calloc failed\n");
+ return 0;
+ }
+
+ base_tv_init(base,fn,fn_fa,samples);
+ /* initialize callbacks */
+#define SET_CALLBACK(fun) base->my_##fun=curses_##fun;
+ SET_CALLBACK(destroy);
+ SET_CALLBACK(mvprintw);
+ SET_CALLBACK(mvaddch);
+ SET_CALLBACK(attron);
+ SET_CALLBACK(attroff);
+ SET_CALLBACK(clear);
+ SET_CALLBACK(colorpair);
+ SET_CALLBACK(drawaln);
+ SET_CALLBACK(loop);
+ SET_CALLBACK(underline);
+#undef SET_CALLBACK
+
+ initscr();
+ keypad(stdscr, TRUE);
+ clear();
+ noecho();
+ cbreak();
+
+ getmaxyx(stdscr, base->mrow, base->mcol);
+ tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
+ tv->whelp = newwin(29, 40, 5, 5);
+
+ 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 base;
+ }
+
+
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; tview with curses is disabled."
+
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
+
+tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ return text_tv_init(fn,fn_fa,samples);
+ }
+#endif // #ifdef _HAVE_CURSES
+
+
--- /dev/null
+#include <unistd.h>
+#include "bam_tview.h"
+
+#define UNDERLINE_FLAG 10
+
+typedef struct HtmlTview {
+ tview_t view;
+ int row_count;
+ tixel_t** screen;
+ FILE* out;
+ int attributes;/* color... */
+ } html_tview_t;
+
+#define FROM_TV(ptr) ((html_tview_t*)ptr)
+
+static void html_destroy(tview_t* base)
+ {
+ int i;
+ html_tview_t* tv=(html_tview_t*)base;
+ if(tv->screen!=NULL)
+ {
+ for(i=0;i< tv->row_count;++i) free(tv->screen[i]);
+ free(tv->screen);
+ }
+ base_tv_destroy(base);
+ free(tv);
+ }
+
+/*
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+ void (*my_)(struct AbstractTview*,int,int,int);
+ void (*my_attron)(struct AbstractTview*,int);
+ void (*my_attroff)(struct AbstractTview*,int);
+ void (*my_clear)(struct AbstractTview*);
+ int (*my_colorpair)(struct AbstractTview*,int);
+*/
+
+static void html_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
+ {
+ int i,nchars=0;
+ unsigned int size=tv->mcol+2;
+ char* str=malloc(size);
+ if(str==0) exit(EXIT_FAILURE);
+ va_list argptr;
+ va_start(argptr, fmt);
+ nchars=vsnprintf(str,size, fmt, argptr);
+ va_end(argptr);
+
+ for(i=0;i< nchars;++i)
+ {
+ tv->my_mvaddch(tv,y,x+i,str[i]);
+ }
+ free(str);
+ }
+
+static void html_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
+ {
+ tixel_t* row=NULL;
+ html_tview_t* ptr=FROM_TV(tv);
+ if( x >= tv->mcol ) return; //out of screen
+ while(ptr->row_count<=y)
+ {
+ int x;
+ row=(tixel_t*)calloc(tv->mcol,sizeof(tixel_t));
+ if(row==0) exit(EXIT_FAILURE);
+ for(x=0;x<tv->mcol;++x) {row[x].ch=' ';row[x].attributes=0;}
+ ptr->screen=(tixel_t**)realloc(ptr->screen,sizeof(tixel_t*)*(ptr->row_count+1));
+ ptr->screen[ptr->row_count++]=row;
+ }
+ row=ptr->screen[y];
+ row[x].ch=ch;
+ row[x].attributes=ptr->attributes;
+ }
+
+static void html_attron(struct AbstractTview* tv,int flag)
+ {
+ html_tview_t* ptr=FROM_TV(tv);
+ ptr->attributes |= flag;
+
+
+ }
+
+static void html_attroff(struct AbstractTview* tv,int flag)
+ {
+ html_tview_t* ptr=FROM_TV(tv);
+ ptr->attributes &= ~(flag);
+ }
+
+static void html_clear(struct AbstractTview* tv)
+ {
+ html_tview_t* ptr=FROM_TV(tv);
+ if(ptr->screen!=NULL)
+ {
+ int i;
+ for(i=0;i< ptr->row_count;++i) free(ptr->screen[i]);
+ free(ptr->screen);
+ ptr->screen=NULL;
+ }
+ ptr->row_count=0;
+ ptr->attributes=0;
+ }
+
+static int html_colorpair(struct AbstractTview* tv,int flag)
+ {
+ return (1 << (flag));
+ }
+
+static int html_drawaln(struct AbstractTview* tv, int tid, int pos)
+ {
+ int y,x;
+ html_tview_t* ptr=FROM_TV(tv);
+ html_clear(tv);
+ base_draw_aln(tv, tid, pos);
+ fputs("<html><head>",ptr->out);
+ fprintf(ptr->out,"<title>%s:%d</title>",
+ tv->header->target_name[tid],
+ pos+1
+ );
+ //style
+
+ fputs("<style type='text/css'>\n",ptr->out);
+ fputs(".tviewbody { margin:5px; background-color:white;text-align:center;}\n",ptr->out);
+ fputs(".tviewtitle {text-align:center;}\n",ptr->out);
+ fputs(".tviewpre { margin:5px; background-color:white;}\n",ptr->out);
+ #define CSS(id,col) fprintf(ptr->out,".tviewc%d {color:%s;}\n.tviewcu%d {color:%s;text-decoration:underline;}\n",id,col,id,col);
+ CSS(0, "black");
+ CSS(1, "blue");
+ CSS(2, "green");
+ CSS(3, "yellow");
+ CSS(4, "black");
+ CSS(5, "green");
+ CSS(6, "cyan");
+ CSS(7, "yellow");
+ CSS(8, "red");
+ CSS(9, "blue");
+ #undef CSS
+ fputs("</style>",ptr->out);
+
+ fputs("</head><body>",ptr->out);
+
+ fprintf(ptr->out,"<div class='tviewbody'><div class='tviewtitle'>%s:%d</div>",
+ tv->header->target_name[tid],
+ pos+1
+ );
+
+ fputs("<pre class='tviewpre'>",ptr->out);
+ for(y=0;y< ptr->row_count;++y)
+ {
+
+ for(x=0;x< tv->mcol;++x)
+ {
+
+
+ if(x== 0 || ptr->screen[y][x].attributes != ptr->screen[y][x-1].attributes)
+ {
+ int css=0;
+ fprintf(ptr->out,"<span");
+ while(css<32)
+ {
+ //if(y>1) fprintf(stderr,"css=%d pow2=%d vs %d\n",css,(1 << (css)),ptr->screen[y][x].attributes);
+ if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0)
+ {
+
+ fprintf(ptr->out," class='tviewc%s%d'",
+ (( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)) )!=0?"u":""),
+ css);
+ break;
+ }
+ ++css;
+ }
+
+
+ fputs(">",ptr->out);
+ }
+
+ int ch=ptr->screen[y][x].ch;
+ switch(ch)
+ {
+ case '<': fputs("<",ptr->out);break;
+ case '>': fputs(">",ptr->out);break;
+ case '&': fputs("&",ptr->out);break;
+ default: fputc(ch,ptr->out); break;
+ }
+
+
+ if(x+1 == tv->mcol || ptr->screen[y][x].attributes!=ptr->screen[y][x+1].attributes)
+ {
+ fputs("</span>",ptr->out);
+ }
+ }
+ if(y+1 < ptr->row_count) fputs("<br/>",ptr->out);
+ }
+ fputs("</pre></div></body></html>",ptr->out);
+ return 0;
+ }
+
+
+#define ANSI_COLOR_RED "\x1b[31m"
+#define ANSI_COLOR_GREEN "\x1b[32m"
+#define ANSI_COLOR_YELLOW "\x1b[33m"
+#define ANSI_COLOR_BLUE "\x1b[34m"
+#define ANSI_COLOR_MAGENTA "\x1b[35m"
+#define ANSI_COLOR_CYAN "\x1b[36m"
+#define ANSI_COLOR_BLACK "\x1b[0m"
+#define ANSI_COLOR_RESET ANSI_COLOR_BLACK
+
+#define ANSI_UNDERLINE_SET "\033[4m"
+#define ANSI_UNDERLINE_UNSET "\033[0m"
+
+static int text_drawaln(struct AbstractTview* tv, int tid, int pos)
+ {
+ int y,x;
+ html_tview_t* ptr=FROM_TV(tv);
+ html_clear(tv);
+ base_draw_aln(tv, tid, pos);
+ int is_term= isatty(fileno(ptr->out));
+
+ for(y=0;y< ptr->row_count;++y)
+ {
+ for(x=0;x< tv->mcol;++x)
+ {
+ if(is_term)
+ {
+ int css=0;
+ while(css<32)
+ {
+ if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0)
+ {
+ break;
+ }
+ ++css;
+ }
+ switch(css)
+ {
+ //CSS(0, "black");
+ case 1: fputs(ANSI_COLOR_BLUE,ptr->out); break;
+ case 2: fputs(ANSI_COLOR_GREEN,ptr->out); break;
+ case 3: fputs(ANSI_COLOR_YELLOW,ptr->out); break;
+ //CSS(4, "black");
+ case 5: fputs(ANSI_COLOR_GREEN,ptr->out); break;
+ case 6: fputs(ANSI_COLOR_CYAN,ptr->out); break;
+ case 7: fputs(ANSI_COLOR_YELLOW,ptr->out); break;
+ case 8: fputs(ANSI_COLOR_RED,ptr->out); break;
+ case 9: fputs(ANSI_COLOR_BLUE,ptr->out); break;
+ default:break;
+ }
+ if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0)
+ {
+ fputs(ANSI_UNDERLINE_SET,ptr->out);
+ }
+
+ }
+
+
+ int ch=ptr->screen[y][x].ch;
+
+ fputc(ch,ptr->out);
+ if(is_term)
+ {
+ fputs(ANSI_COLOR_RESET,ptr->out);
+ if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0)
+ {
+ fputs(ANSI_UNDERLINE_UNSET,ptr->out);
+ }
+ }
+ }
+ fputc('\n',ptr->out);
+ }
+ return 0;
+ }
+
+
+static int html_loop(tview_t* tv)
+ {
+ //tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
+ return 0;
+ }
+
+static int html_underline(tview_t* tv)
+ {
+ return (1 << UNDERLINE_FLAG);
+ }
+
+/*
+static void init_pair(html_tview_t *tv,int id_ge_1, const char* pen, const char* paper)
+ {
+
+ }
+*/
+
+tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ char* colstr=getenv("COLUMNS");
+ html_tview_t *tv = (html_tview_t*)calloc(1, sizeof(html_tview_t));
+ tview_t* base=(tview_t*)tv;
+ if(tv==0)
+ {
+ fprintf(stderr,"Calloc failed\n");
+ return 0;
+ }
+ tv->row_count=0;
+ tv->screen=NULL;
+ tv->out=stdout;
+ tv->attributes=0;
+ base_tv_init(base,fn,fn_fa,samples);
+ /* initialize callbacks */
+#define SET_CALLBACK(fun) base->my_##fun=html_##fun;
+ SET_CALLBACK(destroy);
+ SET_CALLBACK(mvprintw);
+ SET_CALLBACK(mvaddch);
+ SET_CALLBACK(attron);
+ SET_CALLBACK(attroff);
+ SET_CALLBACK(clear);
+ SET_CALLBACK(colorpair);
+ SET_CALLBACK(drawaln);
+ SET_CALLBACK(loop);
+ SET_CALLBACK(underline);
+#undef SET_CALLBACK
+
+
+ if(colstr!=0)
+ {
+ base->mcol=atoi(colstr);
+ if(base->mcol<10) base->mcol=80;
+ }
+ base->mrow=99999;
+
+/*
+ init_pair(tv,1, "blue", "white");
+ init_pair(tv,2, "green", "white");
+ init_pair(tv,3, "yellow", "white");
+ init_pair(tv,4, "white", "white");
+ init_pair(tv,5, "green", "white");
+ init_pair(tv,6, "cyan", "white");
+ init_pair(tv,7, "yellow", "white");
+ init_pair(tv,8, "red", "white");
+ init_pair(tv,9, "blue", "white");
+ */
+ return base;
+ }
+
+
+tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ tview_t* tv=html_tv_init(fn,fn_fa,samples);
+ tv->my_drawaln=text_drawaln;
+ return tv;
+ }
+
extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
extern int bcf_pair_call(const bcf1_t *b);
extern int bcf_min_diff(const bcf1_t *b);
+ extern int bcf_p1_get_M(bcf_p1aux_t *b);
+
+ extern gzFile bcf_p1_fp_lk;
bcf_t *bp, *bout = 0;
bcf1_t *b, *blast;
memset(&vc, 0, sizeof(viewconf_t));
vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1; vc.min_ma_lrt = -1;
memset(qcnt, 0, 8 * 256);
- while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:")) >= 0) {
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
case 'l': vc.bed = bed_read(optarg); break;
case 'C': vc.min_lrt = atof(optarg); break;
case 'X': vc.min_perm_p = atof(optarg); break;
case 'd': vc.min_smpl_frac = atof(optarg); break;
+ case 'K': bcf_p1_fp_lk = gzopen(optarg, "w"); break;
case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
vc.ploidy = calloc(vc.n_sub + 1, 1);
for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
}
}
}
+ if (bcf_p1_fp_lk && p1) {
+ int32_t M = bcf_p1_get_M(p1);
+ gzwrite(bcf_p1_fp_lk, &M, 4);
+ }
while (vcf_read(bp, hin, b) > 0) {
int is_indel, cons_llr = -1;
int64_t cons_gt = -1;
int i;
for (i = 0; i < 9; ++i) em[i] = -1.;
}
- if ( !(vc.flag&VC_KEEPALT) && vc.flag&VC_CALL && vc.min_ma_lrt>=0 )
+ if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
{
bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
int gts = call_multiallelic_gt(b,p1,vc.min_ma_lrt);
}
else if (vc.flag & VC_CALL) { // call variants
bcf_p1rst_t pr;
- int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
+ int calret;
+ gzwrite(bcf_p1_fp_lk, &b->tid, 4);
+ gzwrite(bcf_p1_fp_lk, &b->pos, 4);
+ gzwrite(bcf_p1_fp_lk, &em[0], sizeof(double));
+ calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
if (n_processed % 100000 == 0) {
fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
bcf_p1_dump_afs(p1);
} else bcf_fix_gt(b);
vcf_write(bout, hout, b);
}
+
+ if (bcf_p1_fp_lk) gzclose(bcf_p1_fp_lk);
if (vc.prior_file) free(vc.prior_file);
if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
if (hin != hout) bcf_hdr_destroy(hout);
#include <errno.h>
#include <assert.h>
#include <limits.h>
+#include <zlib.h>
#include "prob1.h"
#include "kstring.h"
#define MC_EM_EPS 1e-5
#define MC_DEF_INDEL 0.15
+gzFile bcf_p1_fp_lk;
+
unsigned char seq_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
return ma;
}
+int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; }
+
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
{
if (n1 == 0 || n1 >= b->n) return -1;
}
}
if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
+ if (bcf_p1_fp_lk)
+ gzwrite(bcf_p1_fp_lk, ma->z, sizeof(double) * (ma->M + 1));
}
static void mc_cal_y(bcf_p1aux_t *ma)
projects / samtools.git / commitdiff