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

fix duplicate PG lines in bwape and bwase

This commit is contained in:
Bradford Powell 2014-01-05 14:54:48 -05:00
parent 10cb6b0507
commit c26ba4e376
3 changed files with 0 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
bwape.c
View File

@ -49,7 +49,6 @@ int bwa_approx_mapQ(const bwa_seq_t *p, int mm);
void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2); void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2);
bntseq_t *bwa_open_nt(const char *prefix); bntseq_t *bwa_open_nt(const char *prefix);
void bwa_print_sam_SQ(const bntseq_t *bns); void bwa_print_sam_SQ(const bntseq_t *bns);
void bwa_print_sam_PG();
pe_opt_t *bwa_init_pe_opt() pe_opt_t *bwa_init_pe_opt()
{ {
@ -671,7 +670,6 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
// core loop // core loop
bwa_print_sam_hdr(bns, rg_line); bwa_print_sam_hdr(bns, rg_line);
bwa_print_sam_PG();
while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt0.mode, opt0.trim_qual)) != 0) { while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt0.mode, opt0.trim_qual)) != 0) {
int cnt_chg; int cnt_chg;
isize_info_t ii; isize_info_t ii;

3
bwase.c
View File

@ -19,8 +19,6 @@
int g_log_n[256]; int g_log_n[256];
void bwa_print_sam_PG();
void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi) void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
{ {
int i, cnt, best; int i, cnt, best;
@ -530,7 +528,6 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
} }
err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa); err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa);
bwa_print_sam_hdr(bns, rg_line); bwa_print_sam_hdr(bns, rg_line);
//bwa_print_sam_PG();
// set ks // set ks
ks = bwa_open_reads(opt.mode, fn_fa); ks = bwa_open_reads(opt.mode, fn_fa);
// core loop // core loop

5
main.c
View File

@ -57,11 +57,6 @@ static int usage()
return 1; return 1;
} }
void bwa_print_sam_PG()
{
err_printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
}
int main(int argc, char *argv[]) int main(int argc, char *argv[])
{ {
int i, ret; int i, ret;