allow to read the prior from the error output. EM iteration is working.

[samtools.git] / bcftools / vcfout.c

diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index fd817f92cbdb279c1f8e5af6ff81b885bab89dc1..f54fde55f8195de0746b372c1a522903cf394b54 100644 (file)
--- a/bcftools/vcfout.c
+++ b/bcftools/vcfout.c
@@ -23,7 +23,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 
 typedef struct {
        int flag, prior_type;
-       char *fn_list;
+       char *fn_list, *prior_file;
        double theta, pref;
 } viewconf_t;
 
@@ -124,10 +124,8 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
        }
        kputc('\0', &s); kputc('\0', &s);
        kputs(b->info, &s);
-       if (p_dp >= 0. && d[2] + d[3] > 0) { // has at least one non-reference base
-               if (b->info[0]) kputc(';', &s);
-               ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
-       }
+       if (b->info[0]) kputc(';', &s);
+       ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
        if (p_hwe <= .2) ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
        if (p_dp >= 0. && p_dp <= .2) ksprintf(&s, ";TDP=%.3lf", p_dp);
        if (p_ed >= 0. && p_ed <= .2) ksprintf(&s, ";TED=%.3lf", p_ed);
@@ -173,6 +171,7 @@ int bcfview(int argc, char *argv[])
                        if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
                        else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
                        else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
+                       else vc.prior_file = strdup(optarg);
                        break;
                }
        }
@@ -206,7 +205,12 @@ int bcfview(int argc, char *argv[])
        vcf_hdr_write(bout, h);
        if (vc.flag & VC_CALL) {
                p1 = bcf_p1_init(h->n_smpl);
-               bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
+               if (vc.prior_file) {
+                       if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
+                               fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__);
+                               return 1;
+                       }
+               } else bcf_p1_init_prior(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)) {
@@ -248,6 +252,7 @@ int bcfview(int argc, char *argv[])
                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);
        bcf_hdr_destroy(h);
        bcf_destroy(b);