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more conservative mapQ

This commit is contained in:
Heng Li 2013-09-09 08:57:45 -04:00
parent 1346f03ff1
commit 1e2cff20ba
1 changed files with 1 additions and 1 deletions
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bwamem.c
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@ -776,7 +776,7 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
} else if (opt->mapQ_coef_len > 0) { } else if (opt->mapQ_coef_len > 0) {
double tmp; double tmp;
tmp = l < opt->mapQ_coef_len? 1. : opt->mapQ_coef_fac / log(l); tmp = l < opt->mapQ_coef_len? 1. : opt->mapQ_coef_fac / log(l);
tmp *= identity; tmp *= a->seedcov < l? (double)a->seedcov / identity : 1;
mapq = (int)(6.02 * (a->score - sub) / opt->a * tmp * tmp + .499); mapq = (int)(6.02 * (a->score - sub) / opt->a * tmp * tmp + .499);
} else { } else {
mapq = (int)(MEM_MAPQ_COEF * (1. - (double)sub / a->score) * log(a->seedcov) + .499); mapq = (int)(MEM_MAPQ_COEF * (1. - (double)sub / a->score) * log(a->seedcov) + .499);