print QUAL as floating numbers

[samtools.git] / bcftools / vcfout.c

diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index 58f11a2e8499ec9f0e888feae7c8aaba6543dfa1..e02e364ca1d2a3921e6900fa0cf4e0c63908d780 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;
 
@@ -88,7 +88,7 @@ static double test_fisher(bcf1_t *b, const char *key, int d[4], int is_single)
        p += 4;
        for (i = 0; i < 4; ++i) {
                d[i] = strtol(p, &p, 10);
-               if (errno == EINVAL || errno == ERANGE) return -2.;
+               if (d[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2.;
                ++p;
        }
        kt_fisher_exact(d[0], d[1], d[2], d[3], &left, &right, &two);
@@ -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);
@@ -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);
@@ -135,8 +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;
 }
@@ -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);