quite a lot changes to the contrast caller, but I still feel something is missing...

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index c5d466e12b164d3df39b093b1cd07377207e2285..9589e891bfdc0ffb86a94c8ab0b7646da620c2d6 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -161,7 +161,7 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
        ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
        ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
        if (a.is_tested) {
-               if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%.4lf,%.4lf,%.2lg,%.2lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
+               if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%lg,%lg,%lg,%lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
                ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
        }
        if (pr->g[0] >= 0. && p_hwe <= .2)
@@ -257,7 +257,10 @@ int bcfview(int argc, char *argv[])
                                return 1;
                        }
                } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
-               if (vc.n1 > 0) bcf_p1_set_n1(p1, vc.n1);
+               if (vc.n1 > 0) {
+                       bcf_p1_set_n1(p1, vc.n1);
+                       bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
+               }
        }
        if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
        if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
@@ -277,7 +280,9 @@ int bcfview(int argc, char *argv[])
                if (hash) {
                        uint64_t x = (uint64_t)b->tid<<32 | b->pos;
                        khint_t k = kh_get(set64, hash, x);
+                       if (kh_size(hash) == 0) break;
                        if (k == kh_end(hash)) continue;
+                       kh_del(set64, hash, k);
                }
                if (tid >= 0) {
                        int l = strlen(b->ref);