fprintf(stderr, "\n");
fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
fprintf(stderr, "Options:\n");
+ fprintf(stderr, " -d display output as (H)tml or (C)urses or (T)ext \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
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;
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);