Update 'samtools depad' help text regarding FASTA reference file

[samtools.git] / bam_tview.c

diff --git a/bam_tview.c b/bam_tview.c
index 81afdfd48ec0372e06f13658f8eff3c00d4d5bf5..06d5e3330ce586cbbbd1eb698176130a52c554b6 100644 (file)
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -284,9 +284,9 @@ static void error(const char *format, ...)
         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
@@ -302,6 +302,8 @@ static void error(const char *format, ...)
 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;
@@ -336,6 +338,10 @@ int bam_tview_main(int argc, char *argv[])
                        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);