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slight modification

This commit is contained in:
Heng Li 2013-09-06 12:37:38 -04:00
parent 623da055e1
commit 451d60f3be
1 changed files with 3 additions and 3 deletions
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6
bwamem.c
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@ -775,9 +775,9 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
mapq = 0;
} else if (opt->mapQ_coef_len > 0) {
double tmp;
tmp = 6.02 * (a->score - sub) / opt->a * identity;
if (l > opt->mapQ_coef_len) tmp *= log(l) / opt->mapQ_coef_fac;
mapq = (int)(tmp + .499);
tmp = l < opt->mapQ_coef_len? 1. : opt->mapQ_coef_fac / log(l);
tmp *= identity;
mapq = (int)(6.02 * (a->score - sub) / opt->a * tmp * tmp + .499);
} else {
mapq = (int)(MEM_MAPQ_COEF * (1. - (double)sub / a->score) * log(a->seedcov) + .499);
mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq;