* changed 3.434 to 4.343 (typo!)

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 995d500eb69ad028a1b0ed2a75da5bde88d92bee..c5d466e12b164d3df39b093b1cd07377207e2285 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=%.2lg,%.2lg,%.2lg,%.2lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
+               if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%.4lf,%.4lf,%.2lg,%.2lg", 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)
@@ -170,7 +170,7 @@ 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;
-       b->qual = r < 1e-100? 99 : -3.434 * log(r);
+       b->qual = r < 1e-100? 99 : -4.343 * log(r);
        if (b->qual > 99) b->qual = 99;
        bcf_sync(n_smpl, b);
        if (!is_var) bcf_shrink_alt(n_smpl, b, 1);
@@ -194,7 +194,7 @@ int bcfview(int argc, char *argv[])
 
        tid = begin = end = -1;
        memset(&vc, 0, sizeof(viewconf_t));
-       vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.9;
+       vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5;
        while ((c = getopt(argc, argv, "1:l:cHAGvLbSuP:t:p:")) >= 0) {
                switch (c) {
                case '1': vc.n1 = atoi(optarg); break;
@@ -285,12 +285,16 @@ int bcfview(int argc, char *argv[])
                        if (b->tid != tid || b->pos >= end) break;
                        if (!(l > begin && end > b->pos)) continue;
                }
+               ++n_processed;
                if (vc.flag & VC_CALL) {
                        bcf_p1rst_t pr;
                        bcf_gl2pl(h->n_smpl, b);
                        bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here
                        if (vc.flag&VC_HWE) bcf_p1_cal_g3(p1, pr.g);
-                       if ((n_processed + 1) % 50000 == 0) bcf_p1_dump_afs(p1);
+                       if (n_processed % 100000 == 0) {
+                               fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
+                               bcf_p1_dump_afs(p1);
+                       }
                        if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
                        update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
                }
@@ -299,7 +303,6 @@ int bcfview(int argc, char *argv[])
                        b->fmt[0] = '\0';
                }
                vcf_write(bout, h, b);
-               ++n_processed;
        }
        if (vc.prior_file) free(vc.prior_file);
        if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);