From 451d60f3be09cc8f4e76537290dd116eff172166 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 6 Sep 2013 12:37:38 -0400 Subject: [PATCH] slight modification --- bwamem.c | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bwamem.c b/bwamem.c index e0aa3e4..0b8ec48 100644 --- a/bwamem.c +++ b/bwamem.c @@ -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;