[med-svn] r14414 - trunk/packages/mira/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-08-09 20:02:25 +0000 (Fri, 09 Aug 2013)
New Revision: 14414

Added:
   trunk/packages/mira/trunk/debian/mirabait.1
Modified:
   trunk/packages/mira/trunk/debian/changelog
Log:
Wrote missing manpage


Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog	2013-08-09 19:17:21 UTC (rev 14413)
+++ trunk/packages/mira/trunk/debian/changelog	2013-08-09 20:02:25 UTC (rev 14414)
@@ -6,6 +6,7 @@
   * debian/mira-assembler.lintian-overrides: deleted unused override
   * debian/rules: Prevent installing duplicated data, rather
     create symlink
+  * debian/mirabait.1: wrote missing manpage
 
  -- Andreas Tille <tille at debian.org>  Fri, 09 Aug 2013 13:59:24 +0200
 

Added: trunk/packages/mira/trunk/debian/mirabait.1
===================================================================
--- trunk/packages/mira/trunk/debian/mirabait.1	                        (rev 0)
+++ trunk/packages/mira/trunk/debian/mirabait.1	2013-08-09 20:02:25 UTC (rev 14414)
@@ -0,0 +1,131 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
+.TH MIRABAIT: "1" "August 2013" "MIRALIB version 3.9.18" "User Commands"
+.SH NAME
+mirabait \- select reads from a read collection
+.SH SYNOPSIS
+.B mirabait
+[\fI\-f <fromtype>\fR] [\fI\-t <totype> [\-t <totype> ...]\fR] [\fI\-iklor\fR] baitfile infile <basename_for_outfile(s)>
+.SH DESCRIPTION
+\fBmirabait\fR selects reads from a read collection which
+are partly similar or equal to sequences defined as target
+baits. Similarity is defined by finding a user-adjustable number of
+common k-mers (sequences of k consecutive bases) which are the same in
+the bait sequences and the screened sequences to be selected, either in forward
+or reverse complement direction.
+.SH OPTIONS
+.TP
+\fB\-f\fR <fromtype>
+load this type of project files, where fromtype is:
+.TP
+caf
+sequences from CAF
+.TP
+maf
+sequences from MAF
+.TP
+phd
+sequences from a PHD
+.TP
+gbf
+sequences from a GBF
+.TP
+fasta
+sequences from a FASTA
+.TP
+fastq
+sequences from a FASTQ
+.TP
+\fB\-t\fR <totype>
+write the sequences to this type (multiple mentions
+of \fB\-t\fR are allowed):
+.TP
+fasta
+sequences to FASTA
+.TP
+fastq
+sequences to FASTQ
+.TP
+caf
+sequences to CAF
+.TP
+maf
+sequences to MAF
+.TP
+txt
+sequence names to text file
+.TP
+\fB\-k\fR
+k\-mer, length of bait in bases (<32, default=31)
+.TP
+\fB\-n\fR
+Min. number of k\-mer baits needed (default=1)
+.TP
+\fB\-i\fR
+Inverse hit: writes only sequences that do not hit bait
+.TP
+\fB\-r\fR
+No checking of reverse complement direction
+.TP
+\fB\-o\fR
+fastq quality Offset (only for \fB\-f\fR = 'fastq')
+Offset of quality values in FASTQ file. Default: 33
+A value of 0 tries to automatically recognise.
+.TP
+\fB\-f\fR <fromtype>
+load this type of project files, where fromtype is:
+.TP
+caf
+sequences from CAF
+.TP
+maf
+sequences from MAF
+.TP
+phd
+sequences from a PHD
+.TP
+gbf
+sequences from a GBF
+.TP
+fasta
+sequences from a FASTA
+.TP
+fastq
+sequences from a FASTQ
+.TP
+\fB\-t\fR <totype>
+write the sequences to this type (multiple mentions
+of \fB\-t\fR are allowed):
+.TP
+fasta
+sequences to FASTA
+.TP
+fastq
+sequences to FASTQ
+.TP
+caf
+sequences to CAF
+.TP
+maf
+sequences to MAF
+.TP
+txt
+sequence names to text file
+.TP
+\fB\-k\fR
+k\-mer, length of bait in bases (<32, default=31)
+.TP
+\fB\-n\fR
+Min. number of k\-mer baits needed (default=1)
+.TP
+\fB\-i\fR
+Inverse hit: writes only sequences that do not hit bait
+.TP
+\fB\-r\fR
+No checking of reverse complement direction
+.TP
+\fB\-o\fR
+fastq quality Offset (only for \fB\-f\fR = 'fastq')
+Offset of quality values in FASTQ file. Default: 33
+A value of 0 tries to automatically recognise.
+.SH AUTHOR
+Bastien Chevreux        (bach at chevreux.org)