X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fcall1.c;fp=bcftools%2Fcall1.c;h=d61d2c46de740cb0162d9d057a4351ddbeb820e9;hb=19bf588b6b3425b1e925a2f837f0b8f351d057d7;hp=cb33e06ef05438fe302ae398ad8de9dbd9ec3130;hpb=50706bea83d8a1518485283876333279f4ae7137;p=samtools.git

diff --git a/bcftools/call1.c b/bcftools/call1.c
index cb33e06..d61d2c4 100644
--- 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;
 	}