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consider the number of suboptimal hits

This commit is contained in:
Heng Li 2013-02-08 17:20:44 -05:00
parent 39607065e0
commit b2c7148dc9
2 changed files with 4 additions and 0 deletions
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3
bwamem.c
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@ -346,6 +346,7 @@ int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a)
int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb;
if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
if (a[j].sub == 0) a[j].sub = a[i].score;
a[j].sub_n += (double)a[i].score / a[j].sub;
break;
}
}
@ -483,7 +484,9 @@ static inline int approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
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 (a->sub) mapq -= (int)(4.343 * log(a->sub_n) + .499);
if (mapq > 60) mapq = 60;
if (mapq < 0) mapq = 0;
return mapq;
}

1
bwamem.h
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@ -33,6 +33,7 @@ typedef struct {
typedef struct {
int64_t rb, re;
int score, qb, qe, seedcov, sub, csub; // sub: suboptimal score; csub: suboptimal inside the chain
double sub_n;
} mem_alnreg_t;
typedef kvec_t(mem_chain_t) mem_chain_v;