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commit 718976bebf88b31a09a1ac5bd12847a91f1cb187 Author: Andreas Tille <[email protected]> Date: Thu Apr 17 11:03:54 2014 +0200 Add manpage --- debian/__manifest__ | 3 --- debian/createmanpages | 6 +++--- debian/manpages | 1 + debian/varscan.1 | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 64 insertions(+), 6 deletions(-) diff --git a/debian/__manifest__ b/debian/__manifest__ deleted file mode 100644 index 86bb3ad..0000000 --- a/debian/__manifest__ +++ /dev/null @@ -1,3 +0,0 @@ -Manifest-Version: 1.0 -Main-Class: net.sf.varscan.VarScan - diff --git a/debian/createmanpages b/debian/createmanpages index 54e3376..4e9364b 100755 --- a/debian/createmanpages +++ b/debian/createmanpages @@ -1,9 +1,9 @@ #!/bin/sh -MANDIR=debian/mans +MANDIR=debian mkdir -p $MANDIR -VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'` +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` help2man --no-info --no-discard-stderr --help-option=" " \ --name='<optional description of the program>' \ - --version-string="$VERSION" <programname> > $MANDIR/<programname>.1 + --version-string="$VERSION" varscan > $MANDIR/varscan.1 diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..0f65186 --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/*.1 diff --git a/debian/varscan.1 b/debian/varscan.1 new file mode 100644 index 0000000..8228036 --- /dev/null +++ b/debian/varscan.1 @@ -0,0 +1,60 @@ +.TH VARSCAN "1" "April 2014" "varscan 2.3.6" "User Commands" +.SH NAME +varscan \- variant detection in next-generation sequencing data +.SH SYNOPSIS +.B varscan +[\fBCOMMAND\fR] [OPTIONS] +.SH DESCRIPTION +Variant detection in massively parallel sequencing. For one sample, +calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, +further classifies each variant as Germline, Somatic, or LOH, and also +detects somatic copy number changes. +.SH USAGE +.SS COMMANDS: +.TP +.B pileup2snp +Identify SNPs from a pileup file +.TP +.B pileup2indel +Identify indels a pileup file +.TP +.B pileup2cns +Call consensus and variants from a pileup file +.TP +.B mpileup2snp +Identify SNPs from an mpileup file +.TP +.B mpileup2indel +Identify indels an mpileup file +.TP +.B mpileup2cns +Call consensus and variants from an mpileup file +.TP +.B somatic +Call germline/somatic variants from tumor\-normal pileups +.TP +.B copynumber +Determine relative tumor copy number from tumor\-normal pileups +.TP +.B readcounts +Obtain read counts for a list of variants from a pileup file +.TP +.B filter +Filter SNPs by coverage, frequency, p\-value, etc. +.TP +.B somaticFilter +Filter somatic variants for clusters/indels +.TP +.B processSomatic +Isolate Germline/LOH/Somatic calls from output +.TP +.B copyCaller +GC\-adjust and process copy number changes from VarScan copynumber output +.TP +.B compare +Compare two lists of positions/variants +.TP +.B limit +Restrict pileup/snps/indels to ROI positions +.SH SEE ALSO +http://varscan.sourceforge.net/using-varscan.html -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/varscan.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
