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

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 4afda56e33d3f8a8f4f9fe511e1d510aade79974..4611af1f995fff8832300af10f733bffa41dd29d 100644 (file)
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -2,8 +2,12 @@
 #include <stdlib.h>
 #include <string.h>
 #include <stdio.h>
+#include <errno.h>
 #include "prob1.h"
 
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
 #define MC_AVG_ERR 0.007
 #define MC_MAX_EM_ITER 16
 #define MC_EM_EPS 1e-4
@@ -54,6 +58,43 @@ void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta)
        }
 }
 
+int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
+{
+       gzFile fp;
+       kstring_t s;
+       kstream_t *ks;
+       long double sum;
+       int dret, k;
+       memset(&s, 0, sizeof(kstring_t));
+       fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+       ks = ks_init(fp);
+       memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
+       while (ks_getuntil(ks, '\n', &s, &dret) >= 0) {
+               if (strstr(s.s, "[afs] ") == s.s) {
+                       char *p = s.s + 6;
+                       for (k = 0; k <= ma->M; ++k) {
+                               int x;
+                               double y;
+                               x = strtol(p, &p, 10);
+                               if (x != k && (errno == EINVAL || errno == ERANGE)) return -1;
+                               ++p;
+                               y = strtod(p, &p);
+                               if (y == 0. && (errno == EINVAL || errno == ERANGE)) return -1;
+                               ma->phi[ma->M - k] += y;
+                       }
+               }
+       }
+       ks_destroy(ks);
+       gzclose(fp);
+       free(s.s);
+       for (sum = 0., k = 0; k <= ma->M; ++k) sum += ma->phi[k];
+       fprintf(stderr, "[prior]");
+       for (k = 0; k <= ma->M; ++k) ma->phi[k] /= sum;
+       for (k = 0; k <= ma->M; ++k) fprintf(stderr, " %d:%.3lg", k, ma->phi[ma->M - k]);
+       fputc('\n', stderr);
+       return 0;
+}
+
 bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
 {
        bcf_p1aux_t *ma;

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 96beb0435806a693357f9d2dc4954857ed7d1065..358f551b4f4bde25a591de96a67a013941a18416 100644 (file)
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -25,6 +25,7 @@ extern "C" {
        int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
        int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
        void bcf_p1_dump_afs(bcf_p1aux_t *ma);
+       int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
 
 #ifdef __cplusplus
 }

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);