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Change the --gender option to --sex
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@pd3
pd3 committed Jan 6, 2017
1 parent e8e369b commit 58678ce
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Showing 3 changed files with 23 additions and 23 deletions.
12 changes: 6 additions & 6 deletions doc/bcftools.1
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@
.\" Title: bcftools
.\" Author: [see the "AUTHORS" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 2017-01-03 08:23 GMT
.\" Date: 2017-01-06 08:12 GMT
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
.TH "BCFTOOLS" "1" "2017\-01\-03 08:23 GMT" "\ \&" "\ \&"
.TH "BCFTOOLS" "1" "2017\-01\-06 08:12 GMT" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Expand Down Expand Up @@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
.SS "VERSION"
.sp
This manual page was last updated \fB2017\-01\-03 08:23 GMT\fR and refers to bcftools git version \fB1\&.3\&.1\-202\-g75da8dd+\fR\&.
This manual page was last updated \fB2017\-01\-06 08:12 GMT\fR and refers to bcftools git version \fB1\&.3\&.1\-206\-ge8e369b+\fR\&.
.SS "BCF1"
.sp
The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
Expand Down Expand Up @@ -1447,7 +1447,7 @@ tag to take values for \&.gen file: GT,PL,GL,GP
output chromosome in the first column instead of CHROM:POS_REF_ALT
.RE
.PP
\fB\-\-gender\fR \fIFILE\fR
\fB\-\-sex\fR \fIFILE\fR
.RS 4
output sex column in the sample file\&. The FILE format is
.RE
Expand Down Expand Up @@ -1530,7 +1530,7 @@ instead of the default
\fI0 \-\fR\&. This is useful for programs which do not handle haploid genotypes correctly\&.
.RE
.PP
\fB\-\-gender\fR \fIFILE\fR
\fB\-\-sex\fR \fIFILE\fR
.RS 4
output sex column in the sample file\&. The FILE format is
.RE
Expand Down Expand Up @@ -1607,7 +1607,7 @@ instead of the default
\fI0 \-\fR\&. This is useful for programs which do not handle haploid genotypes correctly\&.
.RE
.PP
\fB\-\-gender\fR \fIFILE\fR
\fB\-\-sex\fR \fIFILE\fR
.RS 4
output sex column in the sample file\&. The FILE format is
.RE
Expand Down
6 changes: 3 additions & 3 deletions doc/bcftools.txt
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Expand Up @@ -849,7 +849,7 @@ depth information, such as INFO/AD or FORMAT/AD. For that, consider using the
*--chrom*::
output chromosome in the first column instead of CHROM:POS_REF_ALT

*--gender* 'FILE'::
*--sex* 'FILE'::
output sex column in the sample file. The FILE format is
----
MaleSample M
Expand Down Expand Up @@ -896,7 +896,7 @@ depth information, such as INFO/AD or FORMAT/AD. For that, consider using the
default '0 -'. This is useful for programs which do not handle haploid
genotypes correctly.

*--gender* 'FILE'::
*--sex* 'FILE'::
output sex column in the sample file. The FILE format is
----
MaleSample M
Expand Down Expand Up @@ -942,7 +942,7 @@ depth information, such as INFO/AD or FORMAT/AD. For that, consider using the
default '0 -'. This is useful for programs which do not handle haploid
genotypes correctly.

*--gender* 'FILE'::
*--sex* 'FILE'::
output sex column in the sample file. The FILE format is
----
MaleSample M
Expand Down
28 changes: 14 additions & 14 deletions vcfconvert.c
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ struct _args_t
int rev_als, output_vcf_ids, hap2dip, output_chrom_first_col;
int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type;
char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns;
char *outfname, *infname, *ref_fname, *gender_fname;
char *outfname, *infname, *ref_fname, *sex_fname;
int argc, n_threads, record_cmd_line;
};

Expand Down Expand Up @@ -657,12 +657,12 @@ static void hapsample_to_vcf(args_t *args)
fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total);
}

char *init_sample2sex(bcf_hdr_t *hdr, char *gender_fname)
char *init_sample2sex(bcf_hdr_t *hdr, char *sex_fname)
{
int i, nlines;
char *sample2sex = (char*) calloc(bcf_hdr_nsamples(hdr),1);
char **lines = hts_readlist(gender_fname, 1, &nlines);
if ( !lines ) error("Could not read %s\n", gender_fname);
char **lines = hts_readlist(sex_fname, 1, &nlines);
if ( !lines ) error("Could not read %s\n", sex_fname);
for (i=0; i<nlines; i++)
{
char *se = lines[i]; while ( *se && !isspace(*se) ) se++;
Expand All @@ -674,12 +674,12 @@ char *init_sample2sex(bcf_hdr_t *hdr, char *gender_fname)
while ( *se && isspace(*se) ) se++;
if ( *se=='M' ) sample2sex[id] = '1';
else if ( *se=='F' ) sample2sex[id] = '2';
else error("Could not parse %s: %s\n", gender_fname,lines[i]);
else error("Could not parse %s: %s\n", sex_fname,lines[i]);
}
for (i=0; i<nlines; i++) free(lines[i]);
free(lines);
for (i=0; i<bcf_hdr_nsamples(hdr); i++)
if ( !sample2sex[i] ) error("Missing gender for sample %s in %s\n", bcf_hdr_int2id(hdr, BCF_DT_SAMPLE, i),gender_fname);
if ( !sample2sex[i] ) error("Missing sex for sample %s in %s\n", bcf_hdr_int2id(hdr, BCF_DT_SAMPLE, i),sex_fname);
return sample2sex;
}

Expand Down Expand Up @@ -744,7 +744,7 @@ static void vcf_to_gensample(args_t *args)
if (sample_fname)
{
char *sample2sex = NULL;
if ( args->gender_fname ) sample2sex = init_sample2sex(args->header,args->gender_fname);
if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);

int i;
BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
Expand Down Expand Up @@ -869,7 +869,7 @@ static void vcf_to_haplegendsample(args_t *args)
if (sample_fname)
{
char *sample2sex = NULL;
if ( args->gender_fname ) sample2sex = init_sample2sex(args->header,args->gender_fname);
if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);

int i;
BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
Expand Down Expand Up @@ -1016,7 +1016,7 @@ static void vcf_to_hapsample(args_t *args)
if (sample_fname)
{
char *sample2sex = NULL;
if ( args->gender_fname ) sample2sex = init_sample2sex(args->header,args->gender_fname);
if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);

int i;
BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
Expand Down Expand Up @@ -1388,7 +1388,7 @@ static void usage(void)
fprintf(stderr, " -g, --gensample <...> <prefix>|<gen-file>,<sample-file>\n");
fprintf(stderr, " --tag <string> tag to take values for .gen file: GT,PL,GL,GP [GT]\n");
fprintf(stderr, " --chrom output chromosome in first column instead of CHROM:POS_REF_ALT\n");
fprintf(stderr, " --gender <file> output sex column in the sample-file, input format is: Sample\\t[MF]\n");
fprintf(stderr, " --sex <file> output sex column in the sample-file, input format is: Sample\\t[MF]\n");
fprintf(stderr, " --vcf-ids output VCF IDs in second column instead of CHROM:POS_REF_ALT\n");
fprintf(stderr, "\n");
fprintf(stderr, "gVCF conversion:\n");
Expand All @@ -1399,14 +1399,14 @@ static void usage(void)
fprintf(stderr, " --hapsample2vcf <...> <prefix>|<haps-file>,<sample-file>\n");
fprintf(stderr, " --hapsample <...> <prefix>|<haps-file>,<sample-file>\n");
fprintf(stderr, " --haploid2diploid convert haploid genotypes to diploid homozygotes\n");
fprintf(stderr, " --gender <file> output sex column in the sample-file, input format is: Sample\\t[MF]\n");
fprintf(stderr, " --sex <file> output sex column in the sample-file, input format is: Sample\\t[MF]\n");
fprintf(stderr, " --vcf-ids output VCF IDs instead of CHROM:POS_REF_ALT\n");
fprintf(stderr, "\n");
fprintf(stderr, "HAP/LEGEND/SAMPLE conversion:\n");
fprintf(stderr, " -H, --haplegendsample2vcf <...> <prefix>|<hap-file>,<legend-file>,<sample-file>\n");
fprintf(stderr, " -h, --haplegendsample <...> <prefix>|<hap-file>,<legend-file>,<sample-file>\n");
fprintf(stderr, " --haploid2diploid convert haploid genotypes to diploid homozygotes\n");
fprintf(stderr, " --gender <file> output sex column in the sample-file, input format is: Sample\\t[MF]\n");
fprintf(stderr, " --sex <file> output sex column in the sample-file, input format is: Sample\\t[MF]\n");
fprintf(stderr, " --vcf-ids output VCF IDs instead of CHROM:POS_REF_ALT\n");
fprintf(stderr, "\n");
fprintf(stderr, "TSV conversion:\n");
Expand Down Expand Up @@ -1450,7 +1450,7 @@ int main_vcfconvert(int argc, char *argv[])
{"targets-file",required_argument,NULL,'T'},
{"samples",required_argument,NULL,'s'},
{"samples-file",required_argument,NULL,'S'},
{"gender",required_argument,NULL,11},
{"sex",required_argument,NULL,11},
{"gensample",required_argument,NULL,'g'},
{"gensample2vcf",required_argument,NULL,'G'},
{"tag",required_argument,NULL,1},
Expand Down Expand Up @@ -1504,7 +1504,7 @@ int main_vcfconvert(int argc, char *argv[])
case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break;
case 9 : args->n_threads = strtol(optarg, 0, 0); break;
case 10 : args->record_cmd_line = 0; break;
case 11 : args->gender_fname = optarg; break;
case 11 : args->sex_fname = optarg; break;
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
Expand Down

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