From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 24 Apr 2012 08:51:47 +0000 (+0100)
Subject: init_regions: check for non-matching sequence names
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=1ef8ee37fa796dd58e4c18681939a2fafe84ee0c

init_regions: check for non-matching sequence names
---

diff --git a/misc/bamcheck.c b/misc/bamcheck.c
index e5bfb5d..c7db8ab 100644
--- a/misc/bamcheck.c
+++ b/misc/bamcheck.c
@@ -15,7 +15,7 @@
 
 */
 
-#define BAMCHECK_VERSION "2012-04-23"
+#define BAMCHECK_VERSION "2012-04-24"
 
 #define _ISOC99_SOURCE
 #include <stdio.h>
@@ -1082,7 +1082,7 @@ void init_regions(stats_t *stats, char *file)
         if ( iter == kh_end(header_hash) )
         {
             if ( !warned )
-                fprintf(stderr,"Warning: Some sequences not present in the BAM (%s)\n", line);
+                fprintf(stderr,"Warning: Some sequences not present in the BAM, e.g. \"%s\". This message is printed only once.\n", line);
             warned = 1;
             continue;
         }
@@ -1116,6 +1116,7 @@ void init_regions(stats_t *stats, char *file)
         stats->regions[tid].npos++;
     }
     if (line) free(line);
+    if ( !stats->regions ) error("Unable to map the -t sequences to the BAM sequences.\n");
     fclose(fp);
 }