[med-svn] [python-pyvcf] 01/02: Add manpages

[Andreas Tille]

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tille pushed a commit to tag debian/0.6.7-1
in repository python-pyvcf.

commit c782d19d58576fb471885fd90d82e3c64f31e13c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Oct 14 15:11:00 2015 +0200

    Add manpages
---
 debian/pyvcf.manpages |  1 +
 debian/vcf_filter.1   | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/vcf_melt.1     | 14 +++++++++
 3 files changed, 96 insertions(+)

diff --git a/debian/pyvcf.manpages b/debian/pyvcf.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/pyvcf.manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/vcf_filter.1 b/debian/vcf_filter.1
new file mode 100644
index 0000000..fac5434
--- /dev/null
+++ b/debian/vcf_filter.1
@@ -0,0 +1,81 @@
+.TH VCF_FILTER "1" "October 2015" "0.6.7" "User Commands"
+.SH NAME
+vcf_filter \- Filter a VCF file
+.SH SYNOPSIS
+.B vcf_filter
+[\-h] [\-\-no\-short\-circuit] [\-\-no\-filtered]
+[\-\-output OUTPUT] [\-\-local\-script LOCAL_SCRIPT]
+input filter [filter_args] [filter [filter_args]] ...
+.SH DESCRIPTION
+This script is part of PyVCF.
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+input
+File to process (use \- for STDIN) (default: None)
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show this help message and exit. (default: False)
+.TP
+\fB\-\-no\-short\-circuit\fR
+Do not stop filter processing on a site if any filter
+is triggered (default: False)
+.TP
+\fB\-\-output\fR OUTPUT
+Filename to output [STDOUT] (default:
+<_io.TextIOWrapper name='<stdout>' mode='w'
+encoding='ANSI_X3.4\-1968'>)
+.TP
+\fB\-\-no\-filtered\fR
+Output only sites passing the filters (default: False)
+.TP
+\fB\-\-local\-script\fR LOCAL_SCRIPT
+Python file in current working directory with the
+filter classes (default: None)
+.SS "mgq:"
+.IP
+Filters sites with only low quality variants. It is possible to have a
+high site quality with many low quality calls. This filter demands at
+least one call be above a threshold quality.
+.TP
+\fB\-\-genotype\-quality\fR GENOTYPE_QUALITY
+Filter sites with no genotypes above this quality
+(default: 50)
+.SS "snp-only:"
+.IP
+Choose only SNP variants
+.SS "dps:"
+.IP
+Threshold read depth per sample
+.TP
+\fB\-\-depth\-per\-sample\fR DEPTH_PER_SAMPLE
+Minimum required coverage in each sample (default: 5)
+.SS "avg-dps:"
+.IP
+Threshold average read depth per sample (read_depth / sample_count)
+.TP
+\fB\-\-avg\-depth\-per\-sample\fR AVG_DEPTH_PER_SAMPLE
+Minimum required average coverage per sample (default:
+3)
+.SS "eb:"
+.IP
+Filter sites that look like correlated sequencing errors. Some sequencing
+technologies, notably pyrosequencing, produce mutation hotspots where
+there is a constant level of noise, producing some reference and some
+heterozygote calls. This filter computes a Bayes Factor for each site by
+comparing the binomial likelihood of the observed allelic depths under: *
+A model with constant error equal to the MAF. * A model where each sample
+is the ploidy reported by the caller. The test value is the log of the
+bayes factor. Higher values are more likely to be errors. Note: this
+filter requires rpy2
+.TP
+\fB\-\-eblr\fR EBLR
+Filter sites above this error log odds ratio (default:
+\fB\-10\fR)
+.SS "sq:"
+.IP
+Filter low quailty sites
+.TP
+\fB\-\-site\-quality\fR SITE_QUALITY
+Filter sites below this quality (default: 30)
diff --git a/debian/vcf_melt.1 b/debian/vcf_melt.1
new file mode 100644
index 0000000..5a0b4c2
--- /dev/null
+++ b/debian/vcf_melt.1
@@ -0,0 +1,14 @@
+.TH VCF_MELT "1" "October 2015" "0.6.7" "User Commands"
+.SH NAME
+vcf_melt \- Melt a VCF file into a tab delimited set of calls, one per line
+.SH SYNOPSIS
+.B vcf_melt
+<vcf-file>
+.SH DESCRIPTION
+This script is part of PyVCF.
+.P
+VCF files have all the calls from different samples on one line.  This
+script reads vcf on stdin and writes all calls to stdout in tab delimited
+format with one call in one sample per line.  This makes it easy to find
+a given sample's genotype with, say, grep.
+

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