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fix duplicate PG lines in bwape and bwase
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bpow committed Jan 5, 2014
1 parent 10cb6b0 commit c26ba4e
Showing 3 changed files with 0 additions and 10 deletions.
2 changes: 0 additions & 2 deletions bwape.c
Original file line number Diff line number Diff line change
@@ -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);
bntseq_t *bwa_open_nt(const char *prefix);
void bwa_print_sam_SQ(const bntseq_t *bns);
void bwa_print_sam_PG();

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
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) {
int cnt_chg;
isize_info_t ii;
3 changes: 0 additions & 3 deletions bwase.c
Original file line number Diff line number Diff line change
@@ -19,8 +19,6 @@

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)
{
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);
bwa_print_sam_hdr(bns, rg_line);
//bwa_print_sam_PG();
// set ks
ks = bwa_open_reads(opt.mode, fn_fa);
// core loop
5 changes: 0 additions & 5 deletions main.c
Original file line number Diff line number Diff line change
@@ -57,11 +57,6 @@ static int usage()
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 i, ret;

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