Release samtools-0.1.15 (r949:203)

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index cb33e06ef05438fe302ae398ad8de9dbd9ec3130..d61d2c46de740cb0162d9d057a4351ddbeb820e9 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -332,31 +332,34 @@ int bcfview(int argc, char *argv[])
        }
        if (argc == optind) {
                fprintf(stderr, "\n");
-               fprintf(stderr, "Usage:   bcftools view [options] <in.bcf> [reg]\n\n");
-               fprintf(stderr, "Options: -c        SNP calling\n");
-               fprintf(stderr, "         -v        output potential variant sites only (force -c)\n");
-               fprintf(stderr, "         -g        call genotypes at variant sites (force -c)\n");
-               fprintf(stderr, "         -b        output BCF instead of VCF\n");
-               fprintf(stderr, "         -u        uncompressed BCF output (force -b)\n");
-               fprintf(stderr, "         -S        input is VCF\n");
-               fprintf(stderr, "         -A        keep all possible alternate alleles at variant sites\n");
-               fprintf(stderr, "         -G        suppress all individual genotype information\n");
-               fprintf(stderr, "         -N        skip sites where REF is not A/C/G/T\n");
-               fprintf(stderr, "         -Q        output the QCALL likelihood format\n");
-               fprintf(stderr, "         -L        calculate LD for adjacent sites\n");
-               fprintf(stderr, "         -I        skip indels\n");
-               fprintf(stderr, "         -F        PL generated by r921 or before\n");
-               fprintf(stderr, "         -d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]\n");
-               fprintf(stderr, "         -D FILE   sequence dictionary for VCF->BCF conversion [null]\n");
-               fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
-               fprintf(stderr, "         -t FLOAT  scaled substitution mutation rate [%.4g]\n", vc.theta);
-               fprintf(stderr, "         -i FLOAT  indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
-               fprintf(stderr, "         -p FLOAT  variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
-               fprintf(stderr, "         -P STR    type of prior: full, cond2, flat [full]\n");
-               fprintf(stderr, "         -s FILE   list of samples to use [all samples]\n");
-               fprintf(stderr, "         -1 INT    number of group-1 samples [0]\n");
-               fprintf(stderr, "         -U INT    number of permutations for association testing (effective with -1) [0]\n");
-               fprintf(stderr, "         -X FLOAT  only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
+               fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
+               fprintf(stderr, "Input/output options:\n\n");
+               fprintf(stderr, "       -A        keep all possible alternate alleles at variant sites\n");
+               fprintf(stderr, "       -b        output BCF instead of VCF\n");
+               fprintf(stderr, "       -D FILE   sequence dictionary for VCF->BCF conversion [null]\n");
+               fprintf(stderr, "       -F        PL generated by r921 or before (which generate old ordering)\n");
+               fprintf(stderr, "       -G        suppress all individual genotype information\n");
+               fprintf(stderr, "       -l FILE   list of sites (chr pos) or regions (BED) to output [all sites]\n");
+               fprintf(stderr, "       -L        calculate LD for adjacent sites\n");
+               fprintf(stderr, "       -N        skip sites where REF is not A/C/G/T\n");
+               fprintf(stderr, "       -Q        output the QCALL likelihood format\n");
+               fprintf(stderr, "       -s FILE   list of samples to use [all samples]\n");
+               fprintf(stderr, "       -S        input is VCF\n");
+               fprintf(stderr, "       -u        uncompressed BCF output (force -b)\n");
+               fprintf(stderr, "\nConsensus/variant calling options:\n\n");
+               fprintf(stderr, "       -c        SNP calling\n");
+               fprintf(stderr, "       -d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]\n");
+               fprintf(stderr, "       -g        call genotypes at variant sites (force -c)\n");
+               fprintf(stderr, "       -i FLOAT  indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
+               fprintf(stderr, "       -I        skip indels\n");
+               fprintf(stderr, "       -p FLOAT  variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
+               fprintf(stderr, "       -P STR    type of prior: full, cond2, flat [full]\n");
+               fprintf(stderr, "       -t FLOAT  scaled substitution mutation rate [%.4g]\n", vc.theta);
+               fprintf(stderr, "       -v        output potential variant sites only (force -c)\n");
+               fprintf(stderr, "\nContrast calling and association test options:\n\n");
+               fprintf(stderr, "       -1 INT    number of group-1 samples [0]\n");
+               fprintf(stderr, "       -U INT    number of permutations for association testing (effective with -1) [0]\n");
+               fprintf(stderr, "       -X FLOAT  only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
                fprintf(stderr, "\n");
                return 1;
        }