X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fvcfout.c;h=e02e364ca1d2a3921e6900fa0cf4e0c63908d780;hb=05cb7b5bb86b37e82a3ea7868b76031866303da2;hp=f54fde55f8195de0746b372c1a522903cf394b54;hpb=d14782f26230244039bf38f6384a7a9106b0daed;p=samtools.git

diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index f54fde5..e02e364 100644
--- a/bcftools/vcfout.c
+++ b/bcftools/vcfout.c
@@ -109,7 +109,7 @@ static void rm_info(int n_smpl, bcf1_t *b, const char *key)
 static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag)
 {
 	kstring_t s;
-	int d[4], x, is_var = (pr->p_ref < pref);
+	int d[4], is_var = (pr->p_ref < pref);
 	double p_hwe, p_dp, p_ed, r = is_var? pr->p_ref : 1. - pr->p_ref;
 
 	p_hwe = test_hwe(pr->g);
@@ -133,8 +133,8 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 	kputs(b->fmt, &s); kputc('\0', &s);
 	free(b->str);
 	b->m_str = s.m; b->l_str = s.l; b->str = s.s;
-	x = (int)(r < 1e-100? 99 : -3.434 * log(r) + .499);
-	b->qual = x > 99? 99 : x;
+	b->qual = r < 1e-100? 99 : -3.434 * log(r);
+	if (b->qual > 99) b->qual = 99;
 	bcf_sync(n_smpl, b);
 	return is_var;
 }