From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 11 Dec 2009 09:36:18 +0000 (+0000)
Subject: Allow tabs in the CO header field
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=2bcc5f0d7f87c2c46878afe361112ae8e14c53f1;p=samtools.git

Allow tabs in the CO header field
---

diff --git a/sam_header.c b/sam_header.c
index a119c02..3879f3f 100644
--- a/sam_header.c
+++ b/sam_header.c
@@ -345,7 +345,11 @@ static HeaderLine *sam_header_line_parse(const char *headerLine)
         while (*to && *to!='\t') to++;
 
         if ( !required_tags[itype] && !optional_tags[itype] )
+        {
+            // CO is a special case, it can contain anything, including tabs
+            if ( *to ) { to++; continue; }
             tag = new_tag("  ",from,to-1);
+        }
         else
             tag = new_tag(from,from+3,to-1);