-#ifndef _NO_CURSES
-#include <curses.h>
-#include <ctype.h>
#include <assert.h>
-#include <string.h>
-#include "bam.h"
-#include "faidx.h"
-#include "bam_maqcns.h"
+#include "bam_tview.h"
-#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;
- bam_maqcns_t *bmc;
+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;
- char *ref;
-} tview_t;
int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
+ extern unsigned char bam_nt16_table[256];
tview_t *tv = (tview_t*)data;
int i, j, c, rb, attr, max_ins = 0;
uint32_t call = 0;
// 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) 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) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
+ { // call consensus
+ bcf_callret1_t bcr;
+ int qsum[4], a1, a2, tmp;
+ double p[3], prior = 30;
+ bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr);
+ for (i = 0; i < 4; ++i) qsum[i] = bcr.qsum[i]<<2 | i;
+ for (i = 1; i < 4; ++i) // insertion sort
+ for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
+ tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
+ a1 = qsum[0]&3; a2 = qsum[1]&3;
+ p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
+ if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
+ if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
+ if (p[0] < p[1] && p[0] < p[2]) call = (1<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
+ 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);
}
- if (pos%10 == 0) 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;
+ 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) {
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 = 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 c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
} else { // padding
if (j > p->indel) c = '*';
else { // insertion
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 {
+ 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)? ',' : '.';
}
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)
-{
- tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
- tv->is_dot = 1;
- tv->idx = bam_index_load(fn);
- tv->fp = bam_open(fn, "r");
- 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();
-#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(27, 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->rg_hash )
+ {
+ const uint8_t *rg = bam_aux_get(b, "RG");
+ if ( !rg ) return 0;
+ khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
+ if ( k == kh_end(tv->rg_hash) ) return 0;
+ }
+ 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)
-{
+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);
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);
- return 0;
-}
-static void tv_win_goto(tview_t *tv, int *tid, int *pos)
-{
- char str[256];
- 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;
- 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);
+ while (tv->ccol < tv->mcol) {
+ int pos = tv->last_pos + 1;
+ 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_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, "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)
+
+
+static void error(const char *format, ...)
{
- int tid, pos;
- tid = tv->curr_tid; pos = tv->left_pos;
- while (1) {
- 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 '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;
-#endif
- 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;
+ if ( !format )
+ {
+ fprintf(stderr, "\n");
+ 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 group\n");
+ fprintf(stderr, " -d display (H)tml or (C)urses or (T)ext \n");
+ fprintf(stderr, "\n\n");
+ }
+ else
+ {
+ va_list ap;
+ va_start(ap, format);
+ vfprintf(stderr, format, ap);
+ va_end(ap);
+ }
+ 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;
- if (argc == 1) {
- fprintf(stderr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
- return 1;
+ {
+ int view_mode=display_ncurses;
+ tview_t* tv=NULL;
+ char *samples=NULL, *position=NULL;
+ int c;
+ 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);
+
+ 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;
}
- tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
- tv_draw_aln(tv, 0, 0);
- tv_loop(tv);
- tv_destroy(tv);
- return 0;
-}
-#endif
projects / samtools.git / blobdiff