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Uploaded samtools_0.1.16-1_amd64.changes.
[samtools.git]
/
sam_header.c
diff --git
a/sam_header.c
b/sam_header.c
index 05d75deb2c4ced014c6ae5f8612260d05b34660a..f4c8a3bb65d8c52159c16b0a92e1c4d2528e4feb 100644
(file)
--- a/
sam_header.c
+++ b/
sam_header.c
@@
-38,7
+38,7
@@
const char *o_sq_tags[] = {"AS","M5","UR","SP",NULL};
const char *r_sq_tags[] = {"SN","LN",NULL};
const char *u_sq_tags[] = {"SN",NULL};
const char *r_sq_tags[] = {"SN","LN",NULL};
const char *u_sq_tags[] = {"SN",NULL};
-const char *o_rg_tags[] = {"
LB","DS","PU","PI","CN","DT","PL
",NULL};
+const char *o_rg_tags[] = {"
CN","DS","DT","FO","KS","LB","PG","PI","PL","PU","SM
",NULL};
const char *r_rg_tags[] = {"ID",NULL};
const char *u_rg_tags[] = {"ID",NULL};
const char *r_rg_tags[] = {"ID",NULL};
const char *u_rg_tags[] = {"ID",NULL};
@@
-563,6
+563,7
@@
void *sam_header_parse2(const char *headerText)
const char *text;
char *buf=NULL;
size_t nbuf = 0;
const char *text;
char *buf=NULL;
size_t nbuf = 0;
+ int tovalidate = 0;
if ( !headerText )
return 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);
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
// With too many (~250,000) reference sequences the header parsing was too slow with list_append.
hlines = list_append_to_end(hlines, hline);
else