[med-svn] samtools 01/02: Provide some more manpages

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch debian/unstable
in repository samtools.

commit 95188c1fce13f04f507f4ef60c2b6dc8f9355edd
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 21 13:48:54 2015 +0100

    Provide some more manpages
---
 debian/changelog          |  1 +
 debian/mans/ace2sam.1     | 24 ++++++++++++++++++++++++
 debian/mans/samtools.pl.1 | 19 +++++++++++++++++++
 debian/mans/wgsim.1       | 44 ++++++++++++++++++++++++++++++++++++++++++++
 debian/samtools.install   |  1 +
 5 files changed, 89 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 347fe77..1681462 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,7 @@ samtools (1.2-4) UNRELEASED; urgency=medium
   * Fix spelling
   * Fix Mayhem issues caused by unlimited reads of gz input
     Closes: #716199, #716197
+  * Provide some more manpages
 
  -- Andreas Tille <tille at debian.org>  Mon, 21 Dec 2015 13:20:46 +0100
 
diff --git a/debian/mans/ace2sam.1 b/debian/mans/ace2sam.1
new file mode 100644
index 0000000..2aa12a4
--- /dev/null
+++ b/debian/mans/ace2sam.1
@@ -0,0 +1,24 @@
+.TH ACE2SAM "1" "December 2015" "ace2sam 1.2" "User Commands"
+.SH NAME
+ace2sam \- ace to sam converter
+.SH SYNOPSIS
+.B ace2sam
+[\fI\,-pc\/\fR] \fI\,<in.ace>\/\fR
+.SH OPTIONS
+.TP
+\fB\-p\fR
+output padded SAM
+.TP
+\fB\-c\fR
+write the contig sequence in SAM
+.TP
+Notes:
+1. Fields must appear in the following order: (CO\->[BQ]\->(AF)\->(RD\->QA))
+.IP
+2. The order of reads in AF and in RD must be identical
+.IP
+3. Except in BQ, words and numbers must be separated by a single SPACE or TAB
+.IP
+4. This program writes the headerless SAM to stdout and header to stderr
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/samtools.pl.1 b/debian/mans/samtools.pl.1
new file mode 100644
index 0000000..a102ba7
--- /dev/null
+++ b/debian/mans/samtools.pl.1
@@ -0,0 +1,19 @@
+.TH SAMTOOLS.PL "1" "December 2015" "samtools.pl 1.2" "User Commands"
+.SH NAME
+samtools.pl \- helper script for SAMtools
+.SH SYNOPSIS
+.B samtools.pl
+\fI\,<command> \/\fR[\fI\,<arguments>\/\fR]
+.SH DESCRIPTION
+helper script for SAMtools
+.TP
+Command:
+varFilter     filtering SNPs and short indels
+.IP
+pileup2fq     generate fastq from `pileup \fB\-c\fR'
+.IP
+showALEN      print alignment length (ALEN) following CIGAR
+.SH AUTHOR
+THe software was written by Heng Li <lh3 at sanger.ac.uk>
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/wgsim.1 b/debian/mans/wgsim.1
new file mode 100644
index 0000000..b13f121
--- /dev/null
+++ b/debian/mans/wgsim.1
@@ -0,0 +1,44 @@
+.TH WGSIM "1" "December 2015" "wgsim 1.2" "User Commands"
+.SH NAME
+wgsim \- short read simulator
+.SH SYNOPSIS
+.B wgsim
+[\fI\,options\/\fR] \fI\,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/\fR
+.SH OPTIONS
+.TP
+\fB\-e\fR FLOAT
+base error rate [0.020]
+.TP
+\fB\-d\fR INT
+outer distance between the two ends [500]
+.TP
+\fB\-s\fR INT
+standard deviation [50]
+.TP
+\fB\-N\fR INT
+number of read pairs [1000000]
+.TP
+\fB\-1\fR INT
+length of the first read [70]
+.TP
+\fB\-2\fR INT
+length of the second read [70]
+.TP
+\fB\-r\fR FLOAT
+rate of mutations [0.0010]
+.TP
+\fB\-R\fR FLOAT
+fraction of indels [0.15]
+.TP
+\fB\-X\fR FLOAT
+probability an indel is extended [0.30]
+.TP
+\fB\-S\fR INT
+seed for random generator [\-1]
+.TP
+\fB\-h\fR
+haplotype mode
+.SH AUTHOR
+The software was written by Heng Li <lh3 at sanger.ac.uk>
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/samtools.install b/debian/samtools.install
index 98d1583..a227018 100644
--- a/debian/samtools.install
+++ b/debian/samtools.install
@@ -1,2 +1,3 @@
 usr/bin
 usr/share/man/man1
+debian/mans/*.1		usr/share/man/man1
\ No newline at end of file

-- 
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