* fixed a bug in bedidx: input BED not sorted

[samtools.git] / sam_header.c

diff --git a/sam_header.c b/sam_header.c
index 036ea88d28c7b2b82bd05606bbd79120887e86f3..f49b2d463cff3301ee9351ec956a69d6d2c185c4 100644 (file)
--- a/sam_header.c
+++ b/sam_header.c
@@ -351,7 +351,7 @@ static HeaderLine *sam_header_line_parse(const char *headerLine)
 
     while (*to && *to!='\t') to++;
     if ( to-from != 2 ) {
-               debug("[sam_header_line_parse] expected '@XY', got [%s]\n", headerLine);
+               debug("[sam_header_line_parse] expected '@XY', got [%s]\nHint: The header tags must be tab-separated.\n", headerLine);
                return 0;
        }
     
@@ -563,6 +563,7 @@ void *sam_header_parse2(const char *headerText)
     const char *text;
     char *buf=NULL;
     size_t nbuf = 0;
+       int tovalidate = 0;
 
     if ( !headerText )
                return 0;
@@ -571,7 +572,7 @@ void *sam_header_parse2(const char *headerText)
     while ( (text=nextline(&buf, &nbuf, text)) )
     {
         hline = sam_header_line_parse(buf);
-        if ( hline && sam_header_line_validate(hline) )
+        if ( hline && (!tovalidate || sam_header_line_validate(hline)) )
             // With too many (~250,000) reference sequences the header parsing was too slow with list_append.
             hlines = list_append_to_end(hlines, hline);
         else