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minor code simplification

This commit is contained in:
Heng Li 2013-02-13 23:16:16 -05:00
parent 557daabf38
commit 87d619a21f
1 changed files with 9 additions and 4 deletions
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13
bwamem_pair.c
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@ -97,7 +97,12 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *
} }
} }
int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], bwahit_t h[2]) void mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], const mem_alnreg_t *a, int l_ms, const uint8_t *ms, mem_alnreg_v *ma)
{
int is_rev = a->rb >= l_pac? 1 : 0;
}
int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], bwahit_t h[2])
{ {
extern void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h); extern void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h);
pair64_v v; pair64_v v;
@ -108,8 +113,8 @@ int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, cons
for (i = 0; i < a[r].n; ++i) { for (i = 0; i < a[r].n; ++i) {
pair64_t key; pair64_t key;
mem_alnreg_t *e = &a[r].a[i]; mem_alnreg_t *e = &a[r].a[i];
key.x = e->rb < bns->l_pac? e->rb : (bns->l_pac<<1) - 1 - e->rb; // forward position key.x = e->rb < l_pac? e->rb : (l_pac<<1) - 1 - e->rb; // forward position
key.y = (uint64_t)e->score << 32 | i << 2 | (e->rb >= bns->l_pac)<<1 | r; key.y = (uint64_t)e->score << 32 | i << 2 | (e->rb >= l_pac)<<1 | r;
kv_push(pair64_t, v, key); kv_push(pair64_t, v, key);
} }
} }
@ -157,7 +162,7 @@ void mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, c
kstring_t str; kstring_t str;
bwahit_t h[2]; bwahit_t h[2];
str.l = str.m = 0; str.s = 0; str.l = str.m = 0; str.s = 0;
if (mem_pair(opt, bns, pac, pes, s, a, h) == 0) { // successful if (mem_pair(opt, bns->l_pac, pac, pes, s, a, h) == 0) { // successful
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[0], &h[0], opt->is_hard); bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[0], &h[0], opt->is_hard);
s[0].sam = strdup(str.s); str.l = 0; s[0].sam = strdup(str.s); str.l = 0;
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[1], &h[1], opt->is_hard); bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[1], &h[1], opt->is_hard);