tv->mrow = 24; tv->mcol = 80;
tv->color_for = TV_COLOR_MAPQ;
tv->is_dot = 1;
- fprintf(stderr,"Opening '%s'\n",fn);
+
tv->fp = bam_open(fn, "r");
if(tv->fp==0)
{
}
bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
assert(tv->fp);
- fprintf(stderr,"Opening header '%s'\n",fn);
+
tv->header = bam_header_read(tv->fp);
if(tv->header==0)
{
exit(EXIT_FAILURE);
}
tv->idx = bam_index_load(fn);
- if (tv->idx == 0) exit(1);
+ 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);
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 = BAM_TVIEW_UNDERLINE;
+ attr = tv->my_underline(tv);
c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
i = (call&0xffff)/10+1;
if (i > 4) i = 4;
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 |= BAM_TVIEW_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);
}
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
}
c = j? '*' : rb;
if (c == '*') {
- attr = COLOR_PAIR(8);
+ attr = tv->my_colorpair(tv,8);
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,1, tv->ccol++, c);
tv->my_attroff(tv,attr);
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
return 0;
}
+
+
+
+static void error(const char *format, ...)
+{
+ 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[])
+ {
+ 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;
+ }
projects / samtools.git / blobdiff