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[samtools.git] / bcftools / vcfout.c

diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index 37107d097a8e2ff3c42cc0695e786dfa83143f6e..989e831aff90dffc3f53eb984e90bfadca949740 100644 (file)
--- a/bcftools/vcfout.c
+++ b/bcftools/vcfout.c
@@ -126,7 +126,7 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
                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, ";HWE=%.3lf", p_hwe);
+       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);
        kputc('\0', &s);
@@ -172,7 +172,17 @@ int bcfview(int argc, char *argv[])
                }
        }
        if (argc == optind) {
-               fprintf(stderr, "Usage: bcftools view [-cGPb] [-l list] <in.bcf> [reg]\n");
+               fprintf(stderr, "\n");
+               fprintf(stderr, "Usage:   bcftools view [options] <in.bcf> [reg]\n\n");
+               fprintf(stderr, "Options: -c        SNP calling\n");
+               fprintf(stderr, "         -G        suppress all individual genotype information\n");
+               fprintf(stderr, "         -L        discard the PL genotype field\n");
+               fprintf(stderr, "         -v        output potential variant sites only\n");
+               fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
+               fprintf(stderr, "         -t FLOAT  scaled mutation rate [%.4lg]\n", vc.theta);
+               fprintf(stderr, "         -p FLOAT  variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
+               fprintf(stderr, "         -P STR    type of prior: full, cond2, flat [full]\n");
+               fprintf(stderr, "\n");
                return 1;
        }