From 6d9a40f31e3b12c7544233ce0b99747acb78161d Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 21 Jun 2012 08:56:13 +0100 Subject: [PATCH] New -p option to start tview at desired position --- bam_tview.c | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/bam_tview.c b/bam_tview.c index 50bac99..bba732d 100644 --- a/bam_tview.c +++ b/bam_tview.c @@ -440,7 +440,8 @@ void error(const char *format, ...) fprintf(stderr, "\n"); fprintf(stderr, "Usage: bamtk tview [options] [ref.fasta]\n"); fprintf(stderr, "Options:\n"); - fprintf(stderr, " -s STR display only reads from this sample\n"); + fprintf(stderr, " -p chr:pos go directly to this position\n"); + fprintf(stderr, " -s STR display only reads from this sample\n"); fprintf(stderr, "\n\n"); } else @@ -457,17 +458,24 @@ void error(const char *format, ...) int bam_tview_main(int argc, char *argv[]) { tview_t *tv; - char *samples=NULL; + char *samples=NULL, *position=NULL; int c; - while ((c = getopt(argc, argv, "s:")) >= 0) { + while ((c = getopt(argc, argv, "s:p:")) >= 0) { switch (c) { case 's': samples=optarg; break; + case 'p': position=optarg; break; default: error(NULL); } } if (argc==optind) error(NULL); tv = tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples); - tv_draw_aln(tv, 0, 0); + 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; -- 2.39.2