From ebb45dc42ecbdef77ffd5cd45186f0ef74feb5c1 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 11 Mar 2013 21:59:15 -0400 Subject: [PATCH] new code works for SE --- bwamem.c | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bwamem.c b/bwamem.c index 7d45c44..38ab6e6 100644 --- a/bwamem.c +++ b/bwamem.c @@ -874,7 +874,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b s->sam = str.s; } -void mem_aln2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m) +void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m) { kstring_t str; str.l = str.m = 0; str.s = 0; @@ -1024,7 +1024,8 @@ static void *worker2(void *data) if (!(w->opt->flag&MEM_F_PE)) { for (i = w->start; i < w->n; i += w->step) { mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a); - mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0); + //mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0); + mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0); free(w->regs[i].a); } } else {