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missing identical hits; improved sub_n

This commit is contained in:
Heng Li 2013-02-08 17:55:35 -05:00
parent b2c7148dc9
commit 829664d6b5
2 changed files with 7 additions and 6 deletions
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11
bwamem.c
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@ -327,17 +327,18 @@ KSORT_INIT(mem_ar, mem_alnreg_t, alnreg_lt)
int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a)
{ // similar to the loop in mem_chain_flt() { // similar to the loop in mem_chain_flt()
int i, j, m; int i, j, m, tmp;
if (n <= 1) return n; if (n <= 1) return n;
ks_introsort(mem_ar, n, a); ks_introsort(mem_ar, n, a);
for (i = 1; i < n; ++i) { // mark identical hits for (i = 1; i < n; ++i) { // mark identical hits
if (a[i].score == a[i-1].score && a[i].rb == a[i-1].rb && a[i].qb == a[i-1].qb) if (a[i].score == a[i-1].score && a[i].rb == a[i-1].rb && a[i].qb == a[i-1].qb)
a[i].score = 0; a[i].qe = a[i].qb;
} }
for (i = 1, m = 1; i < n; ++i) // exclude identical hits for (i = 1, m = 1; i < n; ++i) // exclude identical hits
if (a[i].score > 0) a[m++] = a[i]; if (a[i].qe > a[i].qb) a[m++] = a[i];
n = m; n = m;
for (i = 0; i < n; ++i) a[i].sub = 0; for (i = 0; i < n; ++i) a[i].sub = 0;
tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
for (i = 1, m = 1; i < n; ++i) { for (i = 1, m = 1; i < n; ++i) {
for (j = 0; j < m; ++j) { for (j = 0; j < m; ++j) {
int b_max = a[j].qb > a[i].qb? a[j].qb : a[i].qb; int b_max = a[j].qb > a[i].qb? a[j].qb : a[i].qb;
@ -346,7 +347,7 @@ 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; 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 (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
if (a[j].sub == 0) a[j].sub = a[i].score; if (a[j].sub == 0) a[j].sub = a[i].score;
a[j].sub_n += (double)a[i].score / a[j].sub; if (a[j].score - a[i].score <= tmp) ++a[j].sub_n;
break; break;
} }
} }
@ -484,7 +485,7 @@ 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; 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; identity = 1. - (double)(l * opt->a - a->score) / (opt->a + opt->b) / l;
mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq; mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq;
if (a->sub) mapq -= (int)(4.343 * log(a->sub_n) + .499); if (a->sub_n) mapq -= (int)(4.343 * log(a->sub_n) + .499);
if (mapq > 60) mapq = 60; if (mapq > 60) mapq = 60;
if (mapq < 0) mapq = 0; if (mapq < 0) mapq = 0;
return mapq; return mapq;

2
bwamem.h
View File

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