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minor improvement to mapQ

This commit is contained in:
Heng Li 2013-02-08 13:43:15 -05:00
parent 245505deed
commit 1bf1a674a8
2 changed files with 23 additions and 9 deletions
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30
bwamem.c
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@ -401,6 +401,15 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
} }
if (a->score < best.score) *a = best; if (a->score < best.score) *a = best;
free(rseq); free(rseq);
// compute seedcov
if (c->n > 1) {
for (i = 0, a->seedcov = 0; i < c->n; ++i) {
s = &c->seeds[i];
if (s->qbeg >= a->qb && s->qbeg + s->len <= a->qe && s->rbeg >= a->rb && s->rbeg + s->len <= a->re) // seed fully contained
a->seedcov += s->len; // this is not very accurate, but for approx. mapQ, this is good enough
}
} else a->seedcov = c->seeds[0].len;
} }
uint32_t *mem_gen_cigar(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar) uint32_t *mem_gen_cigar(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar)
@ -441,6 +450,18 @@ ret_gen_cigar:
* Integrated interface * * Integrated interface *
************************/ ************************/
static inline int 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;
l = a->qe - a->qb > a->re - a->rb? a->qe - a->qb : a->re - a->rb;
mapq = a->score? (int)(MAPQ_COEF * (1. - (double)sub / a->score) * log(a->seedcov) + .499) : 0;
identity = 1. - (double)(l * opt->a - a->score) / (opt->a + opt->b) / l;
mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq;
if (mapq > 60) mapq = 60;
return mapq;
}
void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a) 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 i, k, m; int i, k, m;
@ -471,14 +492,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
if (n_cigar == 0) flag |= 8; if (n_cigar == 0) flag |= 8;
kputs(s->name, &str); kputc('\t', &str); kputw(flag, &str); kputc('\t', &str); kputs(s->name, &str); kputc('\t', &str); kputw(flag, &str); kputc('\t', &str);
kputs(bns->anns[rid].name, &str); kputc('\t', &str); kputuw(pos - bns->anns[rid].offset + 1, &str); kputc('\t', &str); kputs(bns->anns[rid].name, &str); kputc('\t', &str); kputuw(pos - bns->anns[rid].offset + 1, &str); kputc('\t', &str);
{ // approximate mapQ mapq = approx_mapq_se(opt, p);
int sub = p->sub? p->sub : opt->min_seed_len * opt->a;
double identity;
mapq = p->score? (int)(MAPQ_COEF * (1. - (float)sub / p->score) * log(p->score / opt->a) + .499) : 0;
identity = (double)p->score / opt->a / (p->qe - p->qb);
mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq;
if (mapq > 60) mapq = 60;
}
kputw(mapq, &str); kputc('\t', &str); kputw(mapq, &str); kputc('\t', &str);
if (n_cigar) { if (n_cigar) {
int clip5, clip3; int clip5, clip3;

2
bwamem.h
View File

@ -31,7 +31,7 @@ typedef struct {
typedef struct { typedef struct {
int64_t rb, re; int64_t rb, re;
int score, qb, qe, sub; int score, qb, qe, seedcov, sub; // sub: suboptimal score
} mem_alnreg_t; } mem_alnreg_t;
typedef kvec_t(mem_chain_t) mem_chain_v; typedef kvec_t(mem_chain_t) mem_chain_v;