zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #30 from mp15/header_hd 

Add @HD tag to SAM header
This commit is contained in:
Heng Li 2014-08-26 09:44:29 -04:00
parent 1de61b556e ec55ed8d83
commit d9f654908f
1 changed files with 2 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
bwa.c
View File

@ -271,6 +271,7 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line)
{ {
int i; int i;
extern char *bwa_pg; extern char *bwa_pg;
ksprintf(str, "@HD\tVN:1.4\tSO:unknown\n");
for (i = 0; i < bns->n_seqs; ++i) for (i = 0; i < bns->n_seqs; ++i)
err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len); err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
if (rg_line) err_printf("%s\n", rg_line); if (rg_line) err_printf("%s\n", rg_line);
@ -283,6 +284,7 @@ void bwa_format_sam_hdr(const bntseq_t *bns, const char *rg_line, kstring_t *str
int i; int i;
extern char *bwa_pg; extern char *bwa_pg;
str->l = 0; str->s = 0; str->l = 0; str->s = 0;
ksprintf(str, "@HD\tVN:1.4\tSO:unknown\n");
for (i = 0; i < bns->n_seqs; ++i) for (i = 0; i < bns->n_seqs; ++i)
ksprintf(str, "@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len); ksprintf(str, "@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
if (rg_line) ksprintf(str, "%s\n", rg_line); if (rg_line) ksprintf(str, "%s\n", rg_line);