[med-svn] [varscan] 02/02: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository varscan.

commit 718976bebf88b31a09a1ac5bd12847a91f1cb187
Author: Andreas Tille <tille at debian.org>
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

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