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code backup

This commit is contained in:
Heng Li 2013-02-19 00:50:39 -05:00
parent 66585b7982
commit 688872fb1b
3 changed files with 44 additions and 8 deletions
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4
bwamem.c
View File

@ -577,7 +577,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
* Integrated interface *
************************/
static inline int approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
{
int mapq, l, sub = a->sub? a->sub : opt->min_seed_len * opt->a;
double identity;
@ -613,7 +613,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
if (a->a[k].secondary >= 0) continue;
mem_alnreg2hit(&a->a[k], &h);
h.flag |= extra_flag;
h.qual = approx_mapq_se(opt, &a->a[k]);
h.qual = mem_approx_mapq_se(opt, &a->a[k]);
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP);
}
} else bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, 0, opt->flag&MEM_F_HARDCLIP);

1
bwamem.h
View File

@ -6,6 +6,7 @@
#include "utils.h"
#define MEM_MAPQ_COEF 40.0
#define MEM_MAPQ_MAX 60
struct __smem_i;
typedef struct __smem_i smem_i;

47
bwamem_pair.c
View File

@ -159,6 +159,12 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me
return n;
}
static inline double approx_match(const mem_opt_t *opt, const mem_alnreg_v *a)
{
int l = a->qe - a->qb < a->re - a->rb? a->qe - a->qb : a->re - a->rb;
return l - (double)(l * opt->a - a->score) / (opt->a + opt->b);
}
uint64_t 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], int id, uint64_t *sub, int z[2])
{
extern void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h);
@ -219,9 +225,10 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
{
extern void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a);
extern void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag);
extern int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a);
int n = 0, i, j, z[2];
kstring_t str;
bwahit_t h[2];
mem_alnreg_t b[2][2];
uint64_t o, subo;
@ -237,12 +244,40 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
for (i = 0; i < 2; ++i)
for (j = 0; j < 2; ++j)
if (b[i][j].score > 0) n += mem_matesw(opt, bns->l_pac, pac, pes, &b[i][j], s[!i].l_seq, (uint8_t*)s[!i].seq, &a[!i]);
mem_mark_primary_se(opt, a[0].n, a[0].a);
mem_mark_primary_se(opt, a[1].n, a[1].a);
// pairing single-end hits
o = mem_pair(opt, bns->l_pac, pac, pes, s, a, id, &subo, z);
if (0&&o) { // with proper pairing
} else { // no proper pairing
mem_mark_primary_se(opt, a[0].n, a[0].a); mem_sam_se(opt, bns, pac, &s[0], &a[0], 0x41);
mem_mark_primary_se(opt, a[1].n, a[1].a); mem_sam_se(opt, bns, pac, &s[1], &a[1], 0x81);
}
if (o && !(opt->flag&MEM_F_NOPAIRING)) { // with proper pairing
int is_multi[2], q_se[2], q_pe, is_tandem[2];
// check if an end has multiple hits even after mate-SW
for (i = 0; i < 2; ++i) {
for (j = 1; j < a[i].n; ++j)
if (a[i].a[j].secondary < 0) break;
is_multi[i] = j < a[i].n? 1 : 0;
}
if (is_multi[0] || is_multi[1]) goto no_pairing; // TODO: in rare cases, the true hit may be long but with low score
// compute mapQ for the best SE hit
for (i = 0; i < 2; ++i) {
q_se[i] = mem_approx_mapq_se(opt, &a[i].a[0]);
is_tandem[i] = (a[i].a[0].csub > a[i].a[0].sub);
}
q_pe = (int)(MEM_MAPQ_COEF * (1. - (double)(subo>>32) / (o>>32)) * log(a[0].a[z[0]].seedcov + a[1].a[z[1]].seedcov) + .499);
// the following assumes no split hits
if (z[0] == 0 && z[1] == 0) { // the best hit
q_pe = q_pe > q_se[0] + q_se[1]? q_pe : q_se[0] + q_se[1];
q_se[0] = is_tabdem[0]? q_se[0] : q_pe;
q_se[1] = is_tabdem[1]? q_se[1] : q_pe;
} else {
double m[2];
m[0] = approx_match(opt, a[0].a[0]) + approx_match(opt, a[1].a[0]);
m[1] = approx_match(opt, a[0].a[z[0]]) + approx_match(opt, a[1].a[z[1]]);
}
} else goto no_pairing;
return n;
no_pairing:
mem_sam_se(opt, bns, pac, &s[0], &a[0], 0x41);
mem_sam_se(opt, bns, pac, &s[1], &a[1], 0x81);
return n;
}