[med-svn] r11733 - in trunk/packages/genometools/trunk/debian: . man
Sascha Steinbiss
sascha-guest at alioth.debian.org
Wed Jul 11 12:17:19 UTC 2012
Author: sascha-guest
Date: 2012-07-11 12:17:17 +0000 (Wed, 11 Jul 2012)
New Revision: 11733
Added:
trunk/packages/genometools/trunk/debian/genometools.manpages
trunk/packages/genometools/trunk/debian/man/
trunk/packages/genometools/trunk/debian/man/gt-bed_to_gff3.1
trunk/packages/genometools/trunk/debian/man/gt-cds.1
trunk/packages/genometools/trunk/debian/man/gt-chain2dim.1
trunk/packages/genometools/trunk/debian/man/gt-chseqids.1
trunk/packages/genometools/trunk/debian/man/gt-clean.1
trunk/packages/genometools/trunk/debian/man/gt-compreads-compress.1
trunk/packages/genometools/trunk/debian/man/gt-compreads-decompress.1
trunk/packages/genometools/trunk/debian/man/gt-compreads-refcompress.1
trunk/packages/genometools/trunk/debian/man/gt-compreads-refdecompress.1
trunk/packages/genometools/trunk/debian/man/gt-compreads.1
trunk/packages/genometools/trunk/debian/man/gt-congruence-spacedseed.1
trunk/packages/genometools/trunk/debian/man/gt-congruence.1
trunk/packages/genometools/trunk/debian/man/gt-convertseq.1
trunk/packages/genometools/trunk/debian/man/gt-dupfeat.1
trunk/packages/genometools/trunk/debian/man/gt-encseq-bitextract.1
trunk/packages/genometools/trunk/debian/man/gt-encseq-check.1
trunk/packages/genometools/trunk/debian/man/gt-encseq-decode.1
trunk/packages/genometools/trunk/debian/man/gt-encseq-encode.1
trunk/packages/genometools/trunk/debian/man/gt-encseq-info.1
trunk/packages/genometools/trunk/debian/man/gt-encseq-md5.1
trunk/packages/genometools/trunk/debian/man/gt-encseq.1
trunk/packages/genometools/trunk/debian/man/gt-encseq2spm.1
trunk/packages/genometools/trunk/debian/man/gt-eval.1
trunk/packages/genometools/trunk/debian/man/gt-extractfeat.1
trunk/packages/genometools/trunk/debian/man/gt-extractseq.1
trunk/packages/genometools/trunk/debian/man/gt-featureindex.1
trunk/packages/genometools/trunk/debian/man/gt-genomediff.1
trunk/packages/genometools/trunk/debian/man/gt-gff3.1
trunk/packages/genometools/trunk/debian/man/gt-gff3_to_gtf.1
trunk/packages/genometools/trunk/debian/man/gt-gff3validator.1
trunk/packages/genometools/trunk/debian/man/gt-gtf_to_gff3.1
trunk/packages/genometools/trunk/debian/man/gt-id_to_md5.1
trunk/packages/genometools/trunk/debian/man/gt-interfeat.1
trunk/packages/genometools/trunk/debian/man/gt-ltrclustering.1
trunk/packages/genometools/trunk/debian/man/gt-ltrdigest.1
trunk/packages/genometools/trunk/debian/man/gt-ltrharvest.1
trunk/packages/genometools/trunk/debian/man/gt-matchtool.1
trunk/packages/genometools/trunk/debian/man/gt-matstat.1
trunk/packages/genometools/trunk/debian/man/gt-md5_to_id.1
trunk/packages/genometools/trunk/debian/man/gt-merge.1
trunk/packages/genometools/trunk/debian/man/gt-mergefeat.1
trunk/packages/genometools/trunk/debian/man/gt-mgth.1
trunk/packages/genometools/trunk/debian/man/gt-mkfeatureindex.1
trunk/packages/genometools/trunk/debian/man/gt-mkfmindex.1
trunk/packages/genometools/trunk/debian/man/gt-mmapandread.1
trunk/packages/genometools/trunk/debian/man/gt-orffinder.1
trunk/packages/genometools/trunk/debian/man/gt-packedindex-chkintegrity.1
trunk/packages/genometools/trunk/debian/man/gt-packedindex-chksearch.1
trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkctxmap.1
trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkindex.1
trunk/packages/genometools/trunk/debian/man/gt-packedindex-trsuftab.1
trunk/packages/genometools/trunk/debian/man/gt-packedindex.1
trunk/packages/genometools/trunk/debian/man/gt-prebwt.1
trunk/packages/genometools/trunk/debian/man/gt-readjoiner-assembly.1
trunk/packages/genometools/trunk/debian/man/gt-readjoiner-overlap.1
trunk/packages/genometools/trunk/debian/man/gt-readjoiner-prefilter.1
trunk/packages/genometools/trunk/debian/man/gt-readjoiner.1
trunk/packages/genometools/trunk/debian/man/gt-repfind.1
trunk/packages/genometools/trunk/debian/man/gt-scriptfilter.1
trunk/packages/genometools/trunk/debian/man/gt-select.1
trunk/packages/genometools/trunk/debian/man/gt-seq.1
trunk/packages/genometools/trunk/debian/man/gt-seqfilter.1
trunk/packages/genometools/trunk/debian/man/gt-seqids.1
trunk/packages/genometools/trunk/debian/man/gt-seqmutate.1
trunk/packages/genometools/trunk/debian/man/gt-seqorder.1
trunk/packages/genometools/trunk/debian/man/gt-seqstat.1
trunk/packages/genometools/trunk/debian/man/gt-seqtransform.1
trunk/packages/genometools/trunk/debian/man/gt-seqtranslate.1
trunk/packages/genometools/trunk/debian/man/gt-sequniq.1
trunk/packages/genometools/trunk/debian/man/gt-shredder.1
trunk/packages/genometools/trunk/debian/man/gt-shulengthdist.1
trunk/packages/genometools/trunk/debian/man/gt-simreads.1
trunk/packages/genometools/trunk/debian/man/gt-sketch.1
trunk/packages/genometools/trunk/debian/man/gt-sketch_page.1
trunk/packages/genometools/trunk/debian/man/gt-splicesiteinfo.1
trunk/packages/genometools/trunk/debian/man/gt-splitfasta.1
trunk/packages/genometools/trunk/debian/man/gt-stat.1
trunk/packages/genometools/trunk/debian/man/gt-suffixerator.1
trunk/packages/genometools/trunk/debian/man/gt-tagerator.1
trunk/packages/genometools/trunk/debian/man/gt-tallymer-mkindex.1
trunk/packages/genometools/trunk/debian/man/gt-tallymer-occratio.1
trunk/packages/genometools/trunk/debian/man/gt-tallymer-search.1
trunk/packages/genometools/trunk/debian/man/gt-tallymer.1
trunk/packages/genometools/trunk/debian/man/gt-uniq.1
trunk/packages/genometools/trunk/debian/man/gt-uniquesub.1
trunk/packages/genometools/trunk/debian/man/gt.1
Log:
add man pages for GenomeTools
Added: trunk/packages/genometools/trunk/debian/genometools.manpages
===================================================================
--- trunk/packages/genometools/trunk/debian/genometools.manpages (rev 0)
+++ trunk/packages/genometools/trunk/debian/genometools.manpages 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1 @@
+debian/man/*
Added: trunk/packages/genometools/trunk/debian/man/gt-bed_to_gff3.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-bed_to_gff3.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-bed_to_gff3.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: gt-bed_to_gff3
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-BED_TO_GFF3" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-bed_to_gff3 \- Parse BED file and convert it to GFF3\&.
+.SH "SYNOPSIS"
+.sp
+gt bed_to_gff3 [BED_file]
+.SH "OPTIONS"
+.PP
+\fB\-featuretype\fR
+.RS 4
+Set type of parsed BED features (default: BED_feature)
+.RE
+.PP
+\fB\-thicktype\fR
+.RS 4
+Set type of parsed thick BED features (default: BED_thick_feature)
+.RE
+.PP
+\fB\-blocktype\fR
+.RS 4
+Set type of parsed BED blocks (default: BED_block)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-cds.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-cds.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-cds.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,128 @@
+'\" t
+.\" Title: gt-cds
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CDS" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-cds \- Add CDS (coding sequence) features to exon features given in GFF3 file\&.
+.SH "SYNOPSIS"
+.sp
+gt cds [option \&...] [GFF3_file]
+.SH "OPTIONS"
+.PP
+\fB\-minorflen\fR
+.RS 4
+set the minimum length an open reading frame (ORF) must have to be added as a CDS feature (measured in amino acids) (default: 64)
+.RE
+.PP
+\fB\-startcodon\fR
+.RS 4
+require than an ORF must begin with a start codon (default: no)
+.RE
+.PP
+\fB\-finalstopcodon\fR
+.RS 4
+require that the final ORF must end with a stop codon (default: no)
+.RE
+.PP
+\fB\-seqfile\fR
+.RS 4
+set the sequence file from which to extract the features (default: undefined)
+.RE
+.PP
+\fB\-seqfiles\fR
+.RS 4
+set the sequence files from which to extract the features use
+\fI\-\-\fR
+to terminate the list of sequence files
+.RE
+.PP
+\fB\-matchdesc\fR
+.RS 4
+match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) (default: no)
+.RE
+.PP
+\fB\-usedesc\fR
+.RS 4
+use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries\&. If a description contains a sequence range (e\&.g\&., III:1000001\&.\&.2000000), the first part is used as sequence ID (\fIIII\fR) and the first range position as offset (\fI1000001\fR) (default: no)
+.RE
+.PP
+\fB\-regionmapping\fR
+.RS 4
+set file containing sequence\-region to sequence file mapping (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+File format for option \-regionmapping:
+.sp
+The file supplied to option \-regionmapping defines a \(lqmapping\(rq\&. A mapping maps the sequence\-regions given in the GFF3_file to a sequence file containing the corresponding sequence\&. Mappings can be defined in one of the following two forms:
+.sp
+mapping = { chr1 = "hs_ref_chr1\&.fa\&.gz", chr2 = "hs_ref_chr2\&.fa\&.gz" }
+.sp
+or
+.sp
+function mapping(sequence_region) return "hs_ref_"\&.\&.sequence_region\&.\&."\&.fa\&.gz" end
+.sp
+The first form defines a Lua (http://www\&.lua\&.org/) table named \(lqmapping\(rq which maps each sequence region to the corresponding sequence file\&. The second one defines a Lua function \(lqmapping\(rq, which has to return the sequence file name when it is called with the sequence_region as argument\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-chain2dim.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-chain2dim.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-chain2dim.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: gt-chain2dim
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CHAIN2DIM" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-chain2dim \- Chain pairwise matches\&.
+.SH "SYNOPSIS"
+.sp
+gt chain2dim [options] \-m matchfile
+.SH "OPTIONS"
+.PP
+\fB\-m\fR
+.RS 4
+Specify file containing the matches mandatory option (default: undefined)
+.RE
+.PP
+\fB\-global\fR
+.RS 4
+perform global chaining optional parameter gc switches on gap costs (according to L1\-model) optional parameter ov means that overlaps between matches are allowed
+.RE
+.PP
+\fB\-local\fR
+.RS 4
+perform local chaining compute local chains (according to L1\-model)\&. If no parameter is given, compute local chains with maximums score\&. If parameter is given, this must be a positive number optionally followed by the character b or p\&. If only the number, say k, is given, this is the minimum score of the chains output\&. If a number is followed by character b, then output all chains with the largest k scores\&. If a number is followed by character p, then output all chains with scores at most k percent away from the best score\&.
+.RE
+.PP
+\fB\-wf\fR
+.RS 4
+specify weight factor > 0\&.0 to obtain score of a fragment requires one of the options \-localconst \-global gc \-global ov (default: 1\&.00)
+.RE
+.PP
+\fB\-maxgap\fR
+.RS 4
+specify maximal width of gap in chain (default: 0)
+.RE
+.PP
+\fB\-silent\fR
+.RS 4
+do not output the chains but only report their lengths and scores (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-chseqids.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-chseqids.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-chseqids.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,87 @@
+'\" t
+.\" Title: gt-chseqids
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CHSEQIDS" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-chseqids \- Change sequence ids by the mapping given in mapping_file\&.
+.SH "SYNOPSIS"
+.sp
+gt chseqids [option \&...] mapping_file [GFF3_file]
+.SH "OPTIONS"
+.PP
+\fB\-sort\fR
+.RS 4
+sort the GFF3 features after changing the sequence ids (memory consumption is proportional to the input file size) (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+File format for mapping_file:
+.sp
+The supplied mapping file defines a mapping table named \(lqchseqids\(rq\&. It maps the sequence\-regions given in the GFF3_file to other names\&. It can be defined as follows:
+.sp
+chseqids = { chr1 = "seq1", chr2 = "seq2" }
+.sp
+When this example is used, all sequence ids \(lqchr1\(rq will be changed to \(lqseq1\(rq and all sequence ids \(lqchr2\(rq to \(lqseq2\(rq\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-clean.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-clean.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-clean.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,48 @@
+'\" t
+.\" Title: gt-clean
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CLEAN" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-clean \- Remove all files in the current directory which are automatically created by gt\&.
+.SH "SYNOPSIS"
+.sp
+gt clean
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-compreads-compress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-compress.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-compress.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: gt-compreads-compress
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-COMPREADS\-COMPR" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-compreads-compress \- Generates compact encoding for fastq data\&.
+.SH "SYNOPSIS"
+.sp
+gt compreads compress [option \&...] (\-files file [\&...])
+.SH "OPTIONS"
+.PP
+\fB\-descs\fR
+.RS 4
+encode descriptions (default: no)
+.RE
+.PP
+\fB\-files\fR
+.RS 4
+File(s) containing reads\&.
+.RE
+.PP
+\fB\-name\fR
+.RS 4
+specify base name for HCR to be generated\&. Only mandatory, if more than one file was given\&. (default: undefined)
+.RE
+.PP
+\fB\-smap\fR
+.RS 4
+file containing alphabet description\&. If "\-smap" is not set, dna alphabet is used\&. (default: undefined)
+.RE
+.PP
+\fB\-qrange\fR
+.RS 4
+specify range of quality values\&. All values smaller or equal to the lower bound will be converted to the lower bound\&. All values equal or larger than the upper bound will be converted to the upper bound\&. (default: undefined)
+.RE
+.PP
+\fB\-srate\fR
+.RS 4
+sampling rate, set to sensible default depending on sampling method (default: undefined)
+.RE
+.PP
+\fB\-stype\fR
+.RS 4
+type of sampling one of regular \- page \- none (default: page)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-compreads-decompress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-decompress.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-decompress.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-compreads-decompress
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-COMPREADS\-DECOM" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-compreads-decompress \- Decodes a file of compressed reads\&.
+.SH "SYNOPSIS"
+.sp
+gt compreads decompress [option \&...] (\-file file)
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-descs\fR
+.RS 4
+enable description decoding (default: no)
+.RE
+.PP
+\fB\-file\fR
+.RS 4
+specify base name of files containing HCR\&. (default: undefined)
+.RE
+.PP
+\fB\-name\fR
+.RS 4
+specify base name for decoded hcr (suffix will be "\&.fastq") (default: undefined)
+.RE
+.PP
+\fB\-smap\fR
+.RS 4
+specify file containing alphabetdescription (file must be an \&.al1 file)\&. If "\-smap" is not set, dna alphabet is used\&. (default: undefined)
+.RE
+.PP
+\fB\-range\fR
+.RS 4
+decode multiple consecutive reads\&. If range is not specified, the entire file will be decoded\&. (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-compreads-refcompress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-refcompress.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-refcompress.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,93 @@
+'\" t
+.\" Title: gt-compreads-refcompress
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-COMPREADS\-REFCO" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-compreads-refcompress \- Generates compact encoding for fastq data using Reference Compressed Reads (RCR)\&.
+.SH "SYNOPSIS"
+.sp
+gt compreads refcompress [option \&...] (\-bam file \-ref file)
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-mquals\fR
+.RS 4
+store mapping quality for each read (default: no)
+.RE
+.PP
+\fB\-quals\fR
+.RS 4
+store all quality values for each read, this implies enabling of option "vquals" (default: no)
+.RE
+.PP
+\fB\-vquals\fR
+.RS 4
+store quality values of read positions having variations compared to reference (default: no)
+.RE
+.PP
+\fB\-descs\fR
+.RS 4
+store read name for each read (default: no)
+.RE
+.PP
+\fB\-ureads\fR
+.RS 4
+store unmapped reads in a separated fastq file (base name will be the value given in name and suffix will be " _unmapped\&.fastq" (default: no)
+.RE
+.PP
+\fB\-ref\fR
+.RS 4
+Index file (generated by the gt encseq tool) for reference genome\&. (default: undefined)
+.RE
+.PP
+\fB\-bam\fR
+.RS 4
+File containing alignment of reads to genome (sorted "\&.bam" file)\&. (default: undefined)
+.RE
+.PP
+\fB\-name\fR
+.RS 4
+specify base name for RCR to be generated\&. If not set, base name will be set to base name of value given for option "bam" (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-compreads-refdecompress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-refdecompress.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-refdecompress.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-compreads-refdecompress
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-COMPREADS\-REFDE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-compreads-refdecompress \- Decodes a given RCR (Reference Compressed Reads)\&.
+.SH "SYNOPSIS"
+.sp
+gt compreads refdecompress [option \&...] (\-file file)
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-qnames\fR
+.RS 4
+decode read names, default is to just number them (default: no)
+.RE
+.PP
+\fB\-ref\fR
+.RS 4
+Index file (generated by the gt encseq tool) for reference genome\&. (default: undefined)
+.RE
+.PP
+\fB\-rcr\fR
+.RS 4
+specify base name of file containing RCR\&. (default: undefined)
+.RE
+.PP
+\fB\-name\fR
+.RS 4
+specify base name for decoded RCR (suffix will be "\&.rcr\&.decoded") (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-compreads.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,53 @@
+'\" t
+.\" Title: gt-compreads
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-COMPREADS" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-compreads \- Call fastq file compression tool [tool]\&.
+.SH "SYNOPSIS"
+.sp
+gt compreads [option \&...] tool [argument \&...]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Tools:
+.sp
+compress decompress refcompress refdecompress
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-congruence-spacedseed.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-congruence-spacedseed.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-congruence-spacedseed.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-congruence-spacedseed
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CONGRUENCE\-SPAC" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-congruence-spacedseed \- Match spaced seeds\&.
+.SH "SYNOPSIS"
+.sp
+gt congruence spacedseed [options]
+.SH "OPTIONS"
+.PP
+\fB\-esa\fR
+.RS 4
+Specify index (enhanced suffix array) (default: undefined)
+.RE
+.PP
+\fB\-pck\fR
+.RS 4
+Specify index (packed index) (default: undefined)
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Specify files containing the query sequences
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-congruence.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-congruence.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-congruence.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,55 @@
+'\" t
+.\" Title: gt-congruence
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CONGRUENCE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-congruence \- Call congruence tool with name congruence_tool and pass argument(s) to it\&.
+.SH "SYNOPSIS"
+.sp
+gt congruence [option \&...] congruence_tool [argument \&...]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Tools:
+.sp
+spacedseed
+.sp
+For detailed information, please refer to the manual of congruence\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-convertseq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-convertseq.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-convertseq.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,93 @@
+'\" t
+.\" Title: gt-convertseq
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CONVERTSEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-convertseq \- Parse and convert sequence file formats\&.
+.SH "SYNOPSIS"
+.sp
+gt convertseq [options] file [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+reverse complement sequences (default: no)
+.RE
+.PP
+\fB\-showfilelengthvalues\fR
+.RS 4
+show filelengths (default: no)
+.RE
+.PP
+\fB\-noseq\fR
+.RS 4
+do not show sequences (default: no)
+.RE
+.PP
+\fB\-fastawidth\fR
+.RS 4
+FASTA output line width (default: 60)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-dupfeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-dupfeat.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-dupfeat.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-dupfeat
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-DUPFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-dupfeat \- Duplicate internal feature nodes in given GFF3_file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt dupfeat [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-dest\fR
+.RS 4
+set destination type (default: undefined)
+.RE
+.PP
+\fB\-source\fR
+.RS 4
+set source type (default: undefined)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq-bitextract.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-bitextract.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-bitextract.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-encseq-bitextract
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ\-BITEXTRA" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq-bitextract \- Extracts internal data from encoded sequences\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq bitextract [option \&...] [indexname]
+.SH "OPTIONS"
+.PP
+\fB\-mirrored\fR
+.RS 4
+mirror sequence (default: no)
+.RE
+.PP
+\fB\-stoppos\fR
+.RS 4
+output stop positions (default: undefined)
+.RE
+.PP
+\fB\-specialranges\fR
+.RS 4
+output special ranges (default: no)
+.RE
+.PP
+\fB\-bitpos\fR
+.RS 4
+extract and display two bit encoding for position (default: undefined)
+.RE
+.PP
+\fB\-dir\fR
+.RS 4
+specify reading direction (fwd, cpl, rev, rcl) (default: fwd)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq-check.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-check.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-check.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,63 @@
+'\" t
+.\" Title: gt-encseq-check
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ\-CHECK" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq-check \- Check the consistency of an encoded sequence file\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq check [option \&...] [file]
+.SH "OPTIONS"
+.PP
+\fB\-scantrials\fR
+.RS 4
+specify number of scan trials (default: 0)
+.RE
+.PP
+\fB\-multicharcmptrials\fR
+.RS 4
+specify number of multicharacter trials (default: 0)
+.RE
+.PP
+\fB\-prefixlength\fR
+.RS 4
+prefix length (default: 0)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq-decode.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-decode.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-decode.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,94 @@
+'\" t
+.\" Title: gt-encseq-decode
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ\-DECODE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq-decode \- Decode/extract encoded sequences\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq decode (sequence_file|indexname)
+.SH "OPTIONS"
+.PP
+\fB\-mirrored\fR
+.RS 4
+virtually append the reverse complement of each sequence (default: no)
+.RE
+.PP
+\fB\-lossless\fR
+.RS 4
+allow lossless original sequence retrieval (default: no)
+.RE
+.PP
+\fB\-dir\fR
+.RS 4
+specify reading direction (fwd, cpl, rev, rcl) (default: fwd)
+.RE
+.PP
+\fB\-seq\fR
+.RS 4
+extract sequence identified by its number (default: undefined)
+.RE
+.PP
+\fB\-seqrange\fR
+.RS 4
+extract multiple consecutive sequences (default: undefined)
+.RE
+.PP
+\fB\-output\fR
+.RS 4
+specify output format (choose from fasta|concat) (default: fasta)
+.RE
+.PP
+\fB\-range\fR
+.RS 4
+concatenated range to extract (implies
+\fI\-output concat\fR) (default: undefined)
+.RE
+.PP
+\fB\-sepchar\fR
+.RS 4
+specify character to print as SEPARATOR (default: |)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq-encode.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-encode.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-encode.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,113 @@
+'\" t
+.\" Title: gt-encseq-encode
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ\-ENCODE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq-encode \- Encode sequence files efficiently\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq encode sequence_file [sequence_file [sequence_file \&...]]
+.SH "OPTIONS"
+.PP
+\fB\-showstats\fR
+.RS 4
+show compression results (default: no)
+.RE
+.PP
+\fB\-ssp\fR
+.RS 4
+output sequence separator positions to file (default: yes)
+.RE
+.PP
+\fB\-des\fR
+.RS 4
+output sequence descriptions to file (default: yes)
+.RE
+.PP
+\fB\-sds\fR
+.RS 4
+output sequence description separator positions to file (default: yes)
+.RE
+.PP
+\fB\-md5\fR
+.RS 4
+output MD5 sums to file (default: yes)
+.RE
+.PP
+\fB\-sat\fR
+.RS 4
+specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
+.RE
+.PP
+\fB\-dna\fR
+.RS 4
+input is DNA sequence (default: no)
+.RE
+.PP
+\fB\-protein\fR
+.RS 4
+input is protein sequence (default: no)
+.RE
+.PP
+\fB\-indexname\fR
+.RS 4
+specify name for index to be generated (default: undefined)
+.RE
+.PP
+\fB\-smap\fR
+.RS 4
+specify file containing a symbol mapping (default: undefined)
+.RE
+.PP
+\fB\-lossless\fR
+.RS 4
+allow lossless original sequence retrieval (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq-info.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-info.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-info.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: gt-encseq-info
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ\-INFO" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq-info \- Display meta\-information about an encoded sequence\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq info [option \&...] indexname
+.SH "OPTIONS"
+.PP
+\fB\-nomap\fR
+.RS 4
+do not map encoded sequence (gives less information) (default: no)
+.RE
+.PP
+\fB\-mirrored\fR
+.RS 4
+use mirrored encoded sequence (DNA only) (default: no)
+.RE
+.PP
+\fB\-noindexname\fR
+.RS 4
+do not output index name (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq-md5.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-md5.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-md5.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-encseq-md5
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ\-MD5" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq-md5 \- Display MD5 sums for an encoded sequence\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq md5 [option \&...] indexname
+.SH "OPTIONS"
+.PP
+\fB\-fromindex\fR
+.RS 4
+use MD5 table from \&.md5 file (default: yes)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,53 @@
+'\" t
+.\" Title: gt-encseq
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq \- Call encoded sequence manipulation tool [tool] and pass argument(s) to it\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq [option \&...] tool [argument \&...]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Tools:
+.sp
+bitextract check decode encode info md5
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq2spm.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq2spm.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq2spm.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,87 @@
+'\" t
+.\" Title: gt-encseq2spm
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ2SPM" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-encseq2spm \- Compute suffix prefix matches from encoded sequence\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq2spm [option \&...] [file]
+.SH "OPTIONS"
+.PP
+\fB\-l\fR
+.RS 4
+specify the minimum length (default: 0)
+.RE
+.PP
+\fB\-parts\fR
+.RS 4
+specify the number of parts (default: 0)
+.RE
+.PP
+\fB\-memlimit\fR
+.RS 4
+specify maximal amount of memory to be used during index construction (in bytes, the keywords
+\fIMB\fR
+and
+\fIGB\fR
+are allowed) (default: undefined)
+.RE
+.PP
+\fB\-singlestrand\fR
+.RS 4
+use only the forward strand of the sequence (default: no)
+.RE
+.PP
+\fB\-spm\fR
+.RS 4
+specify output for spms (default: undefined)
+.RE
+.PP
+\fB\-ii\fR
+.RS 4
+specify the input sequence (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-eval.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-eval.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-eval.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,91 @@
+'\" t
+.\" Title: gt-eval
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-EVAL" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-eval \- Compare annotation files and show accuracy measures (prediction vs\&. reference)\&.
+.SH "SYNOPSIS"
+.sp
+gt eval reference_file prediction_file
+.SH "OPTIONS"
+.PP
+\fB\-nuc\fR
+.RS 4
+evaluate nucleotide level (memory consumption is proportional to the input file sizes) (default: yes)
+.RE
+.PP
+\fB\-ltr\fR
+.RS 4
+evaluate a LTR retrotransposon prediction instead of a gene prediction (all LTR_retrotransposon elements are considered to have an undetermined strand) (default: no)
+.RE
+.PP
+\fB\-ltrdelta\fR
+.RS 4
+set allowed delta for LTR borders to be considered equal (default: 20)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+The program shows sensitivity and specificity values for certain feature types (e\&.g\&., gene, mRNA, and exon)\&. For some feature types the number of missing and wrong features of that type is also shown\&. Thereby, \(lqmissing\(rq means the number of features of that type from the \(lqreference\(rq without overlap to a feature of that type from the \(lqprediction\(rq\&. Vice versa, \(lqwrong\(rq denotes the number of features of that type from the \(lqprediction\(rq without overlap to a feature of that type from the \(lqreference\(rq\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-extractfeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-extractfeat.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-extractfeat.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,143 @@
+'\" t
+.\" Title: gt-extractfeat
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-EXTRACTFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-extractfeat \- Extract features given in GFF3 file from sequence file\&.
+.SH "SYNOPSIS"
+.sp
+gt extractfeat [option \&...] [GFF3_file]
+.SH "OPTIONS"
+.PP
+\fB\-type\fR
+.RS 4
+set type of features to extract (default: undefined)
+.RE
+.PP
+\fB\-join\fR
+.RS 4
+join feature sequences in the same subgraph into a single one (default: no)
+.RE
+.PP
+\fB\-translate\fR
+.RS 4
+translate the features (of a DNA sequence) into protein (default: no)
+.RE
+.PP
+\fB\-seqid\fR
+.RS 4
+add sequence ID of extracted features to FASTA descriptions (default: no)
+.RE
+.PP
+\fB\-target\fR
+.RS 4
+add target ID(s) of extracted features to FASTA descriptions (default: no)
+.RE
+.PP
+\fB\-seqfile\fR
+.RS 4
+set the sequence file from which to extract the features (default: undefined)
+.RE
+.PP
+\fB\-seqfiles\fR
+.RS 4
+set the sequence files from which to extract the features use
+\fI\-\-\fR
+to terminate the list of sequence files
+.RE
+.PP
+\fB\-matchdesc\fR
+.RS 4
+match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) (default: no)
+.RE
+.PP
+\fB\-usedesc\fR
+.RS 4
+use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries\&. If a description contains a sequence range (e\&.g\&., III:1000001\&.\&.2000000), the first part is used as sequence ID (\fIIII\fR) and the first range position as offset (\fI1000001\fR) (default: no)
+.RE
+.PP
+\fB\-regionmapping\fR
+.RS 4
+set file containing sequence\-region to sequence file mapping (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+File format for option \-regionmapping:
+.sp
+The file supplied to option \-regionmapping defines a \(lqmapping\(rq\&. A mapping maps the sequence\-regions given in the GFF3_file to a sequence file containing the corresponding sequence\&. Mappings can be defined in one of the following two forms:
+.sp
+mapping = { chr1 = "hs_ref_chr1\&.fa\&.gz", chr2 = "hs_ref_chr2\&.fa\&.gz" }
+.sp
+or
+.sp
+function mapping(sequence_region) return "hs_ref_"\&.\&.sequence_region\&.\&."\&.fa\&.gz" end
+.sp
+The first form defines a Lua (http://www\&.lua\&.org/) table named \(lqmapping\(rq which maps each sequence region to the corresponding sequence file\&. The second one defines a Lua function \(lqmapping\(rq, which has to return the sequence file name when it is called with the sequence_region as argument\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-extractseq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-extractseq.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-extractseq.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,144 @@
+'\" t
+.\" Title: gt-extractseq
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-EXTRACTSEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-extractseq \- Extract sequences from given sequence file(s) or fastaindex\&.
+.SH "SYNOPSIS"
+.sp
+gt extractseq [option \&...] [sequence_file(s)] | fastaindex
+.SH "OPTIONS"
+.PP
+\fB\-frompos\fR
+.RS 4
+extract sequence from this position counting from 1 on (default: 0)
+.RE
+.PP
+\fB\-topos\fR
+.RS 4
+extract sequence up to this position counting from 1 on (default: 0)
+.RE
+.PP
+\fB\-match\fR
+.RS 4
+extract all sequences whose description matches the given pattern\&. The given pattern must be a valid extended regular expression\&. (default: undefined)
+.RE
+.PP
+\fB\-keys\fR
+.RS 4
+extract substrings for keys in specified file (default: undefined)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+The option \-keys allows to extract substrings or sequences from the given sequence file or from a fasta index\&. The substrings to be extracted are specified in a key file given as argument to this option\&. The key file must contain lines of the form
+.sp
+k
+.sp
+or
+.sp
+k i j
+.sp
+where k is a string (the key) and the optional i and j are positive integers such that i⇐j\&. k is the key and the optional numbers i and j specify the first position of the substring and the last position of the substring to be extracted\&. The positions are counted from 1\&. If k is identical to the string between the first first and second occurrence of the symbol | in a fasta header, then the fasta header and the corresponding sequence is output\&. For example in the fasta header
+.sp
+>tr|A0AQI4|A0AQI4_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1
+.sp
+the fasta key is A0AQI4\&. If i and j are both specified, then the corresponding substring is shown in fasta format\&. In the latter case the header of the fasta formatted sequence in the output begins with
+.sp
+>k i j
+.sp
+followed by the original original fasta header\&. If the sequence input are fasta files, then the following holds: \- duplicated lines in the input file lead to only one sequence in the output \- the sequences are output according to the order in the original sequence files \- the formatting of the output can be controlled by the options \-width, \-o, \-gzip, and \-bzip2
+.sp
+If the sequence input comes from a fasta index (see below), the following holds: \- option \-width is required \- option \-o, \-gzip and \-bzip2 do not work \- the sequences are output in the order the corresponding keys appear in the key file
+.sp
+If the end of the argument list only contains one filename, say fastaindex, then it is checked if there is a file fastaindex\&.kys\&. This makes up part of the fasta index, which is contructed by calling the suffixerator tool as follows:
+.sp
+gt suffixerator \-protein \-ssp \-tis \-des \-sds \-kys \-indexname fastaindex \-db inputfile1 [inputfile2 \&.\&.]
+.sp
+This reads the protein sequence files given to the option \-db and creates several files: \- a file fastaindex\&.esq representing the sequence\&. \- a file fastaindex\&.ssp specifying the sequence separator positions\&. \- a file fastaindex\&.des showing the fasta headers line by line\&. \- a file fastaindex\&.sds giving the sequence header delimiter positions\&. \- a file fastaindex\&.kys containing the keys in the fasta files\&.
+.sp
+For the suffixerator command to work, the keys of the form |key| in the fasta header must satisfy the following constraints:
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+they all have to be of the same length, not longer than 128, and not shorter than 1
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+they have to appear in lexicographic order
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-featureindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-featureindex.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-featureindex.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-featureindex
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-FEATUREINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-featureindex \- Retrieve annotations from a persistent feature index as GFF3 output\&.
+.SH "SYNOPSIS"
+.sp
+gt featureindex [option \&...] indexfilename
+.SH "OPTIONS"
+.PP
+\fB\-range\fR
+.RS 4
+range constraint for index query (default: undefined)
+.RE
+.PP
+\fB\-seqid\fR
+.RS 4
+sequence region (default: undefined)
+.RE
+.PP
+\fB\-retain\fR
+.RS 4
+retain attributes (default: yes)
+.RE
+.PP
+\fB\-backend\fR
+.RS 4
+database backend to use choose from [sqlite] (default: sqlite)
+.RE
+.PP
+\fB\-filename\fR
+.RS 4
+filename for feature database (sqlite backend only) (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-genomediff.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-genomediff.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-genomediff.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,80 @@
+'\" t
+.\" Title: gt-genomediff
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-GENOMEDIFF" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-genomediff \- Calculates shulens of Genomes and the Kr\&.
+.SH "SYNOPSIS"
+.sp
+gt genomediff [option \&...] \-pck|\-esa indexname
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-esa\fR
+.RS 4
+Specify index (enhanced suffix array) (default: undefined)
+.RE
+.PP
+\fB\-pck\fR
+.RS 4
+Specify index (packed index) (default: undefined)
+.RE
+.PP
+\fB\-unitfile\fR
+.RS 4
+specifies genomic units, File is in lua\-format like this: units = { genome1 = { "file1", "file2" }, genome2 = { "file3", "file4" } } only give basenames of the files! comment lines start with
+\fI\-\-\fR
+and will be ignored\&. (default: undefined)
+.RE
+.PP
+\fB\-scan\fR
+.RS 4
+do not load esa index but scan it sequentially (default: yes)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <willrodt at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-gff3.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gff3.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-gff3.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,144 @@
+'\" t
+.\" Title: gt-gff3
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-GFF3" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-gff3 \- Parse, possibly transform, and output GFF3 files\&.
+.SH "SYNOPSIS"
+.sp
+gt gff3 [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-sort\fR
+.RS 4
+sort the GFF3 features (memory consumption is proportional to the input file size(s)) (default: no)
+.RE
+.PP
+\fB\-tidy\fR
+.RS 4
+try to tidy the GFF3 files up during parsing (default: no)
+.RE
+.PP
+\fB\-retainids\fR
+.RS 4
+when available, use the original IDs provided in the source file (memory consumption is proportional to the input file size(s)) (default: no)
+.RE
+.PP
+\fB\-checkids\fR
+.RS 4
+make sure the ID attributes are unique within the scope of each GFF3_file, as required by GFF3 specification (memory consumption is proportional to the input file size(s)) (default: no)
+.RE
+.PP
+\fB\-addids\fR
+.RS 4
+add missing "##sequence\-region" lines automatically (default: yes)
+.RE
+.PP
+\fB\-fixregionboundaries\fR
+.RS 4
+automatically adjust "##sequence\-region" lines to contain all their features (memory consumption is proportional to the input file size(s)) (default: no)
+.RE
+.PP
+\fB\-addintrons\fR
+.RS 4
+add intron features between existing exon features (default: no)
+.RE
+.PP
+\fB\-offset\fR
+.RS 4
+transform all features by the given offset (default: undefined)
+.RE
+.PP
+\fB\-offsetfile\fR
+.RS 4
+transform all features by the offsets given in file (default: undefined)
+.RE
+.PP
+\fB\-typecheck\fR
+.RS 4
+check GFF3 types against "id" and "name" tags in given OBO file (default: undefined)
+.RE
+.PP
+\fB\-show\fR
+.RS 4
+show GFF3 output (default: yes)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+File format for option \-offsetfile:
+.sp
+The file supplied to option \-offsetfile defines a mapping table named \(lqoffsets\(rq\&. It maps the sequence\-regions given in the GFF3_file to offsets\&. It can be defined as follows:
+.sp
+offsets = { chr1 = 1000, chr2 = 500 }
+.sp
+When this example is used, all features with seqid \(lqchr1\(rq will be offset by 1000 and all features with seqid \(lqchr2\(rq by 500\&.
+.sp
+If \-offsetfile is used, offsets for all sequence\-regions contained in the given GFF3 files must be defined\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-gff3_to_gtf.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gff3_to_gtf.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-gff3_to_gtf.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-gff3_to_gtf
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-GFF3_TO_GTF" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-gff3_to_gtf \- Parse GFF3 file(s) and show them as GTF2\&.2\&.
+.SH "SYNOPSIS"
+.sp
+gt gff3_to_gtf [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-gff3validator.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gff3validator.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-gff3validator.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,53 @@
+'\" t
+.\" Title: gt-gff3validator
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-GFF3VALIDATOR" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-gff3validator \- Strictly validate given GFF3 files\&.
+.SH "SYNOPSIS"
+.sp
+gt gff3validator [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-typecheck\fR
+.RS 4
+check GFF3 types against "id" and "name" tags in given OBO file (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-gtf_to_gff3.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gtf_to_gff3.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-gtf_to_gff3.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-gtf_to_gff3
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-GTF_TO_GFF3" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-gtf_to_gff3 \- Parse GTF2\&.2 file and convert it to GFF3\&.
+.SH "SYNOPSIS"
+.sp
+gt gtf_to_gff3 [GTF_file]
+.SH "OPTIONS"
+.PP
+\fB\-tidy\fR
+.RS 4
+try to tidy the GTF file up during parsing (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-id_to_md5.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-id_to_md5.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-id_to_md5.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,118 @@
+'\" t
+.\" Title: gt-id_to_md5
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ID_TO_MD5" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-id_to_md5 \- Change sequence IDs in given GFF3 files to MD5 fingerprints of the corresponding sequences\&.
+.SH "SYNOPSIS"
+.sp
+gt id_to_md5 [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-seqfile\fR
+.RS 4
+set the sequence file from which to extract the features (default: undefined)
+.RE
+.PP
+\fB\-seqfiles\fR
+.RS 4
+set the sequence files from which to extract the features use
+\fI\-\-\fR
+to terminate the list of sequence files
+.RE
+.PP
+\fB\-matchdesc\fR
+.RS 4
+match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) (default: no)
+.RE
+.PP
+\fB\-usedesc\fR
+.RS 4
+use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries\&. If a description contains a sequence range (e\&.g\&., III:1000001\&.\&.2000000), the first part is used as sequence ID (\fIIII\fR) and the first range position as offset (\fI1000001\fR) (default: no)
+.RE
+.PP
+\fB\-regionmapping\fR
+.RS 4
+set file containing sequence\-region to sequence file mapping (default: undefined)
+.RE
+.PP
+\fB\-subtargetids\fR
+.RS 4
+substitute the target IDs with MD5 sums (default: yes)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+File format for option \-regionmapping:
+.sp
+The file supplied to option \-regionmapping defines a \(lqmapping\(rq\&. A mapping maps the sequence\-regions given in the GFF3_file to a sequence file containing the corresponding sequence\&. Mappings can be defined in one of the following two forms:
+.sp
+mapping = { chr1 = "hs_ref_chr1\&.fa\&.gz", chr2 = "hs_ref_chr2\&.fa\&.gz" }
+.sp
+or
+.sp
+function mapping(sequence_region) return "hs_ref_"\&.\&.sequence_region\&.\&."\&.fa\&.gz" end
+.sp
+The first form defines a Lua (http://www\&.lua\&.org/) table named \(lqmapping\(rq which maps each sequence region to the corresponding sequence file\&. The second one defines a Lua function \(lqmapping\(rq, which has to return the sequence file name when it is called with the sequence_region as argument\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-interfeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-interfeat.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-interfeat.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-interfeat
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-INTERFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-interfeat \- Add intermediary features between outside features in given GFF3 file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt interfeat [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-outside\fR
+.RS 4
+set outside type (default: exon)
+.RE
+.PP
+\fB\-inter\fR
+.RS 4
+set intermediary type (default: intron)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-ltrclustering.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-ltrclustering.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-ltrclustering.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-ltrclustering
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-LTRCLUSTERING" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-ltrclustering \- Cluster features of LTRs\&.
+.SH "SYNOPSIS"
+.sp
+gt ltrclustering [option \&...] indexname [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-psmall\fR
+.RS 4
+specify how many percent of the smaller sequence a match needs to cover in order to cluster the two sequences of the match\&. (default: 0)
+.RE
+.PP
+\fB\-plarge\fR
+.RS 4
+specify how many percent of the larger sequence a match needs to cover in order to cluster the two sequences of the match\&. (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-ltrdigest.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-ltrdigest.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-ltrdigest.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,138 @@
+'\" t
+.\" Title: gt-ltrdigest
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-LTRDIGEST" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-ltrdigest \- Identifies and annotates sequence features in LTR retrotransposon candidates\&.
+.SH "SYNOPSIS"
+.sp
+gt ltrdigest [option \&...] gff3_file indexname
+.SH "OPTIONS"
+.PP
+\fB\-outfileprefix\fR
+.RS 4
+prefix for output files (e\&.g\&.
+\fIfoo\fR
+will create files called
+\fIfoo_*\&.csv\fR
+and
+\fIfoo_*\&.fas\fR) Omit this option for GFF3 output only\&.
+.RE
+.PP
+\fB\-seqnamelen\fR
+.RS 4
+set maximal length of sequence names in FASTA headers (e\&.g\&. for clustalw or similar tools) (default: 20)
+.RE
+.PP
+\fB\-pptlen\fR
+.RS 4
+required PPT length range (default: 8 30)
+.RE
+.PP
+\fB\-uboxlen\fR
+.RS 4
+required U\-box length range (default: 3 30)
+.RE
+.PP
+\fB\-pptradius\fR
+.RS 4
+radius around beginning of 3\*(Aq LTR to search for PPT (default: 30)
+.RE
+.PP
+\fB\-trnas\fR
+.RS 4
+tRNA library in multiple FASTA format for PBS detection Omit this option to disable PBS search\&.
+.RE
+.PP
+\fB\-pbsalilen\fR
+.RS 4
+required PBS/tRNA alignment length range (default: 11 30)
+.RE
+.PP
+\fB\-pbsoffset\fR
+.RS 4
+allowed PBS offset from LTR boundary range (default: 0 5)
+.RE
+.PP
+\fB\-pbstrnaoffset\fR
+.RS 4
+allowed PBS/tRNA 3\*(Aq end alignment offset range (default: 0 5)
+.RE
+.PP
+\fB\-pbsmaxedist\fR
+.RS 4
+maximal allowed PBS/tRNA alignment unit edit distance (default: 1)
+.RE
+.PP
+\fB\-pbsradius\fR
+.RS 4
+radius around end of 5\*(Aq LTR to search for PBS (default: 30)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-ltrharvest.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-ltrharvest.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-ltrharvest.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,177 @@
+'\" t
+.\" Title: gt-ltrharvest
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-LTRHARVEST" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-ltrharvest \- Predict LTR retrotransposons\&.
+.SH "SYNOPSIS"
+.sp
+gt ltrharvest [option \&...] \-index <indexname>
+.SH "OPTIONS"
+.PP
+\fB\-index\fR
+.RS 4
+specify the name of the enhanced suffix array index (mandatory) (default: undefined)
+.RE
+.PP
+\fB\-range\fR
+.RS 4
+specify range in the input sequence(s) in which LTR pairs are searched (default: 0 0)
+.RE
+.PP
+\fB\-seed\fR
+.RS 4
+specify minimum seed length for exact repeats (default: 30)
+.RE
+.PP
+\fB\-minlenltr\fR
+.RS 4
+specify minimum length for each LTR (default: 100)
+.RE
+.PP
+\fB\-maxlenltr\fR
+.RS 4
+specify maximum length for each LTR (default: 1000)
+.RE
+.PP
+\fB\-mindistltr\fR
+.RS 4
+specify minimum distance of LTR startpositions (default: 1000)
+.RE
+.PP
+\fB\-maxdistltr\fR
+.RS 4
+specify maximum distance of LTR startpositions (default: 15000)
+.RE
+.PP
+\fB\-similar\fR
+.RS 4
+specify similaritythreshold in range [1\&.\&.100%] (default: 85\&.00)
+.RE
+.PP
+\fB\-mintsd\fR
+.RS 4
+specify minimum length for each TSD (default: 4)
+.RE
+.PP
+\fB\-maxtsd\fR
+.RS 4
+specify maximum length for each TSD (default: 20)
+.RE
+.PP
+\fB\-motif\fR
+.RS 4
+specify 2 nucleotides startmotif + 2 nucleotides endmotif:
+\fB*\fR* (default: undefined)
+.RE
+.PP
+\fB\-motifmis\fR
+.RS 4
+specify maximum number of mismatches in motif [0,3] (default: 4)
+.RE
+.PP
+\fB\-vic\fR
+.RS 4
+specify the number of nucleotides (to the left and to the right) that will be searched for TSDs and/or motifs around 5\*(Aq and 3\*(Aq boundary of predicted LTR retrotransposons (default: 60)
+.RE
+.PP
+\fB\-overlaps\fR
+.RS 4
+specify no|best|all (default: best)
+.RE
+.PP
+\fB\-xdrop\fR
+.RS 4
+specify xdropbelowscore for extension\-alignment (default: 5)
+.RE
+.PP
+\fB\-mat\fR
+.RS 4
+specify matchscore for extension\-alignment (default: 2)
+.RE
+.PP
+\fB\-mis\fR
+.RS 4
+specify mismatchscore for extension\-alignment (default: \-2)
+.RE
+.PP
+\fB\-ins\fR
+.RS 4
+specify insertionscore for extension\-alignment (default: \-3)
+.RE
+.PP
+\fB\-del\fR
+.RS 4
+specify deletionscore for extension\-alignment (default: \-3)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+verbose mode (default: no)
+.RE
+.PP
+\fB\-longoutput\fR
+.RS 4
+additional motif/TSD output (default: no)
+.RE
+.PP
+\fB\-out\fR
+.RS 4
+specify FASTA outputfilename (default: undefined)
+.RE
+.PP
+\fB\-outinner\fR
+.RS 4
+specify FASTA outputfilename for inner regions (default: undefined)
+.RE
+.PP
+\fB\-gff3\fR
+.RS 4
+specify GFF3 outputfilename (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+For detailed information, please refer to the manual of ltrharvest\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-matchtool.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-matchtool.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-matchtool.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,80 @@
+'\" t
+.\" Title: gt-matchtool
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MATCHTOOL" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-matchtool \- Parse match formats and/or invoke matching tools\&.
+.SH "SYNOPSIS"
+.sp
+gt matchtool [option \&...]
+.SH "OPTIONS"
+.PP
+\fB\-type\fR
+.RS 4
+choose match file format: OPENMATCH:
+\fIopen match\fR
+format, e\&.g\&. vmatch BLASTOUT : tabular BLAST output (\-m 8) BLASTALLP: invoke BLASTALL with blastp BLASTALLN: invoke BLASTALL with blastn BLASTP : invoke blastp BLASTN : invoke blastn LAST : invoke LAST SW : use Smith\-Waterman (default: OPENMATCH)
+.RE
+.PP
+\fB\-matchfile\fR
+.RS 4
+set input file name (default: undefined)
+.RE
+.PP
+\fB\-db\fR
+.RS 4
+set database file name (default: undefined)
+.RE
+.PP
+\fB\-swminlen\fR
+.RS 4
+set minimum required alignment length (for Smith\-Waterman alignment) (default: 10)
+.RE
+.PP
+\fB\-swmaxedist\fR
+.RS 4
+set maximum allowed edit distance (for Smith\-Waterman alignment) (default: 0)
+.RE
+.PP
+\fB\-query\fR
+.RS 4
+set query file name (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-matstat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-matstat.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-matstat.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,86 @@
+'\" t
+.\" Title: gt-matstat
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MATSTAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-matstat \- Compute matching statistics\&.
+.SH "SYNOPSIS"
+.sp
+gt matstat [options \&...] \-query queryfile [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-fmi\fR
+.RS 4
+specify fmindex (default: undefined)
+.RE
+.PP
+\fB\-esa\fR
+.RS 4
+specify suffix array (default: undefined)
+.RE
+.PP
+\fB\-pck\fR
+.RS 4
+specify packed index (default: undefined)
+.RE
+.PP
+\fB\-query\fR
+.RS 4
+specify queryfiles
+.RE
+.PP
+\fB\-min\fR
+.RS 4
+only output length if >= given minimum length (default: 0)
+.RE
+.PP
+\fB\-max\fR
+.RS 4
+only output length if ⇐ given maximum length (default: 0)
+.RE
+.PP
+\fB\-output\fR
+.RS 4
+set output flags (sequence, querypos, subjectpos)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+For detailed information, please refer to the manual of matstat\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-md5_to_id.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-md5_to_id.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-md5_to_id.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-md5_to_id
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MD5_TO_ID" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-md5_to_id \- Change MD5 fingerprints used as sequence IDs in given GFF3 files to ``regular\*(Aq\*(Aq ones\&.
+.SH "SYNOPSIS"
+.sp
+gt md5_to_id [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-merge.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-merge.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-merge.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-merge
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MERGE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-merge \- Merge sorted GFF3 files in sorted fashion\&.
+.SH "SYNOPSIS"
+.sp
+gt merge [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-mergefeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mergefeat.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-mergefeat.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-mergefeat
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MERGEFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-mergefeat \- Merge adjacent features without children of the same type in given GFF3 file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt mergefeat [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-mgth.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mgth.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-mgth.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,146 @@
+'\" t
+.\" Title: gt-mgth
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MGTH" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-mgth \- Metagenomethreader, for predicting genes in metagenomeprojects\&.
+.SH "SYNOPSIS"
+.sp
+gt mgth [option \&...] XML\-File Query\-FASTA\-File Hit\-FASTA\-File
+.SH "OPTIONS"
+.PP
+\fB\-s\fR
+.RS 4
+score for synonymic base exchanges (default: 1\&.00)
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+score for non\-synonymic base exchanges (default: \-1\&.00)
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+score for blast\-hit\-end within query sequence (default: \-10\&.00)
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+score for stop\-codon within querysequence (default: \-2\&.00)
+.RE
+.PP
+\fB\-h\fR
+.RS 4
+score for stop\-codon within hitsequence (default: \-5\&.00)
+.RE
+.PP
+\fB\-l\fR
+.RS 4
+score for leaving a gene on forward/reverse strand or enter a gene on forward/reverse strand (default: \-2\&.00)
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+max\&. span between coding\-regions resume as one prediction (default: 400\&.00)
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+max\&. span between coding\-regions in different reading frames resume as coding\-regions in the optimal reading\-frame (default: 200\&.00)
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+db\-name for fcgi\-db (default: nucleotide)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+name for resulting output\-file (default: output)
+.RE
+.PP
+\fB\-k\fR
+.RS 4
+name for the Hit\-Sequence\-DB (default: nucleotide database)
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+true or false if a Hit\-FASTA\-File exist (default: no)
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+format of the output\-file (default: 1)
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+minimum length of the as\-sequence (default: 15)
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+minimum percent\-value for hit\-statistic\-output (default: 0\&.00)
+.RE
+.PP
+\fB\-e\fR
+.RS 4
+use of alternative start\-codons (default: 1)
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+search for homology (default: no)
+.RE
+.PP
+\fB\-g\fR
+.RS 4
+testmodus, output without creating date (default: no)
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+extend the EGTs to max (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+For detailed information, please refer to the manual of mgth\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-mkfeatureindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mkfeatureindex.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-mkfeatureindex.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-mkfeatureindex
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MKFEATUREINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-mkfeatureindex \- Creates a new FeatureIndex from annotation data\&.
+.SH "SYNOPSIS"
+.sp
+gt mkfeatureindex [option \&...] <input filename(s)>
+.SH "OPTIONS"
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-backend\fR
+.RS 4
+database backend to use choose from [sqlite] (default: sqlite)
+.RE
+.PP
+\fB\-input\fR
+.RS 4
+input data format choose from gff|bed|gtf (default: gff)
+.RE
+.PP
+\fB\-filename\fR
+.RS 4
+filename for feature database (sqlite backend only) (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-mkfmindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mkfmindex.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-mkfmindex.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-mkfmindex
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MKFMINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-mkfmindex \- Compute FM\-index\&.
+.SH "SYNOPSIS"
+.sp
+gt mkfmindex [option \&...] \-ii indexfile [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-fmout\fR
+.RS 4
+specify name of FM\-index to be generated (mandatory if more than one input index is specified) (default: undefined)
+.RE
+.PP
+\fB\-ii\fR
+.RS 4
+specify indices to be used
+.RE
+.PP
+\fB\-size\fR
+.RS 4
+specify size (tiny, small, medium, big) (default: medium)
+.RE
+.PP
+\fB\-noindexpos\fR
+.RS 4
+store no index positions (hence the positions of matches in the index cannot be retrieved) (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-mmapandread.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mmapandread.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-mmapandread.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,48 @@
+'\" t
+.\" Title: gt-mmapandread
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-MMAPANDREAD" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-mmapandread \- Map the supplied files into memory and read them once\&.
+.SH "SYNOPSIS"
+.sp
+gt mmapandread file [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-orffinder.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-orffinder.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-orffinder.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,94 @@
+'\" t
+.\" Title: gt-orffinder
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ORFFINDER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-orffinder \- Identifies ORFs (open reading frames) in sequences\&.
+.SH "SYNOPSIS"
+.sp
+gt orffinder [option \&...] indexname [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-types\fR
+.RS 4
+Specify regions which should be searched for open reading frames, e\&.g\&.
+\fILTR_retrotransposon\fR
+.RE
+.PP
+\fB\-allorfs\fR
+.RS 4
+search for all ORFs instead of only the longest (default: no)
+.RE
+.PP
+\fB\-min\fR
+.RS 4
+minimum length of ORF (default: 30)
+.RE
+.PP
+\fB\-max\fR
+.RS 4
+maximum length of ORF (default: 10000)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-packedindex-chkintegrity.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-chkintegrity.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-chkintegrity.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-packedindex-chkintegrity
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-PACKEDINDEX\-CHK" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-packedindex-chkintegrity \- Map [indexname] block composition indexand bwt and check index integrity\&.
+.SH "SYNOPSIS"
+.sp
+gt packedindex chkintegrity indexname
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+print verbose progress information (default: no)
+.RE
+.PP
+\fB\-skip\fR
+.RS 4
+number of symbols to skip (default: 0)
+.RE
+.PP
+\fB\-ticks\fR
+.RS 4
+print dot after this many symbols tested okay (default: 100000)
+.RE
+.PP
+\fB\-ext\-rank\-check\fR
+.RS 4
+do additional checks of rank query results (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-packedindex-chksearch.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-chksearch.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-chksearch.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,123 @@
+'\" t
+.\" Title: gt-packedindex-chksearch
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-PACKEDINDEX\-CHK" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-packedindex-chksearch \- Load (or build if necessary) BWT index for project [indexname] and perform verification of search results\&.
+.SH "SYNOPSIS"
+.sp
+gt packedindex chksearch indexname
+.SH "OPTIONS"
+.PP
+\fB\-bsize\fR
+.RS 4
+specify size of blocks (default: 8)
+.RE
+.PP
+\fB\-blbuck\fR
+.RS 4
+specify number of blocks per bucket (default: 8)
+.RE
+.PP
+\fB\-locfreq\fR
+.RS 4
+specify the locate frequency parameter i means that each i\-th position of input string is stored 0 ⇒ no locate information (default: 16)
+.RE
+.PP
+\fB\-locbitmap\fR
+.RS 4
+marked/unmarked positions for locate are stored as bitmaps this gives faster location of hits but increases the index by 1 bit per symbol (default: yes)
+.RE
+.PP
+\fB\-sprank\fR
+.RS 4
+build rank table for special symbols this produces an index which can be used to regenerate the original sequence but increases the memory used during index creation (default: no)
+.RE
+.PP
+\fB\-sprankilog\fR
+.RS 4
+specify the interval of rank sampling as log value parameter i means that each 2^i\-th position of source is sampled for rank undefined ⇒ chooses default of log(log(sequence length)) (default: undefined)
+.RE
+.PP
+\fB\-ctxilog\fR
+.RS 4
+specify the interval of context sampling as log value parameter i means that each 2^i\-th position of source is sampled for rank \-1 ⇒ chooses default of log(log(sequence length)) \-2 ⇒ generates no map (default: \-2)
+.RE
+.PP
+\fB\-minpatlen\fR
+.RS 4
+minimum length of patterns searched for, \-1 implies automatic choice based on index properties (default: \-1)
+.RE
+.PP
+\fB\-maxpatlen\fR
+.RS 4
+maximum length of patterns searched for, \-1 implies automatic choice based on index properties (default: \-1)
+.RE
+.PP
+\fB\-nsamples\fR
+.RS 4
+number of sequences to search for (default: 1000)
+.RE
+.PP
+\fB\-chksfxarray\fR
+.RS 4
+verify integrity of stored suffix array positions (default: no)
+.RE
+.PP
+\fB\-full\-lfmap\fR
+.RS 4
+verify complete backwards regeneration of original sequence (default: no)
+.RE
+.PP
+\fB\-chkcontext\fR
+.RS 4
+verify integrity of regenerated sequence context (default: no)
+.RE
+.PP
+\fB\-ticks\fR
+.RS 4
+print dot after this many symbols tested okay (default: 100000)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+print verbose progress information (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkctxmap.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkctxmap.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkctxmap.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,58 @@
+'\" t
+.\" Title: gt-packedindex-mkctxmap
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-PACKEDINDEX\-MKC" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-packedindex-mkctxmap \- Build BWT packedindex for project [indexname]\&.
+.SH "SYNOPSIS"
+.sp
+gt packedindex mkctxmap indexname
+.SH "OPTIONS"
+.PP
+\fB\-ctxilog\fR
+.RS 4
+specify the interval of context sampling as log value parameter i means that each 2^i\-th position of source is sampled for rank \-1 ⇒ chooses default of log(log(sequence length)) \-2 ⇒ generates no map (default: \-2)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+print verbose progress information (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkindex.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkindex.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,183 @@
+'\" t
+.\" Title: gt-packedindex-mkindex
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-PACKEDINDEX\-MKI" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-packedindex-mkindex \- Compute packed index\&.
+.SH "SYNOPSIS"
+.sp
+gt packedindex mkindex [option \&...] (\-db file [\&...] | \-ii index)
+.SH "OPTIONS"
+.PP
+\fB\-ssp\fR
+.RS 4
+output sequence separator positions to file (default: yes)
+.RE
+.PP
+\fB\-des\fR
+.RS 4
+output sequence descriptions to file (default: yes)
+.RE
+.PP
+\fB\-sds\fR
+.RS 4
+output sequence description separator positions to file (default: yes)
+.RE
+.PP
+\fB\-md5\fR
+.RS 4
+output MD5 sums to file (default: yes)
+.RE
+.PP
+\fB\-sat\fR
+.RS 4
+specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
+.RE
+.PP
+\fB\-dna\fR
+.RS 4
+input is DNA sequence (default: no)
+.RE
+.PP
+\fB\-protein\fR
+.RS 4
+input is protein sequence (default: no)
+.RE
+.PP
+\fB\-indexname\fR
+.RS 4
+specify name for index to be generated (default: undefined)
+.RE
+.PP
+\fB\-db\fR
+.RS 4
+specify database files
+.RE
+.PP
+\fB\-smap\fR
+.RS 4
+specify file containing a symbol mapping (default: undefined)
+.RE
+.PP
+\fB\-lossless\fR
+.RS 4
+allow lossless original sequence retrieval (default: no)
+.RE
+.PP
+\fB\-mirrored\fR
+.RS 4
+virtually append the reverse complement of each sequence (default: no)
+.RE
+.PP
+\fB\-pl\fR
+.RS 4
+specify prefix length for bucket sort recommendation: use without argument; then a reasonable prefix length is automatically determined (default: 0)
+.RE
+.PP
+\fB\-dc\fR
+.RS 4
+specify difference cover value (default: 0)
+.RE
+.PP
+\fB\-kys\fR
+.RS 4
+output/sort according to keys of the form |key| in fasta header (default: nosort)
+.RE
+.PP
+\fB\-bsize\fR
+.RS 4
+specify size of blocks (default: 8)
+.RE
+.PP
+\fB\-blbuck\fR
+.RS 4
+specify number of blocks per bucket (default: 8)
+.RE
+.PP
+\fB\-locfreq\fR
+.RS 4
+specify the locate frequency parameter i means that each i\-th position of input string is stored 0 ⇒ no locate information (default: 16)
+.RE
+.PP
+\fB\-locbitmap\fR
+.RS 4
+marked/unmarked positions for locate are stored as bitmaps this gives faster location of hits but increases the index by 1 bit per symbol (default: yes)
+.RE
+.PP
+\fB\-sprank\fR
+.RS 4
+build rank table for special symbols this produces an index which can be used to regenerate the original sequence but increases the memory used during index creation (default: no)
+.RE
+.PP
+\fB\-sprankilog\fR
+.RS 4
+specify the interval of rank sampling as log value parameter i means that each 2^i\-th position of source is sampled for rank undefined ⇒ chooses default of log(log(sequence length)) (default: undefined)
+.RE
+.PP
+\fB\-ctxilog\fR
+.RS 4
+specify the interval of context sampling as log value parameter i means that each 2^i\-th position of source is sampled for rank \-1 ⇒ chooses default of log(log(sequence length)) \-2 ⇒ generates no map (default: \-2)
+.RE
+.PP
+\fB\-dir\fR
+.RS 4
+specify reading direction (fwd, cpl, rev, rcl) (default: fwd)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-showprogress\fR
+.RS 4
+show a progress bar (default: no)
+.RE
+.PP
+\fB\-ii\fR
+.RS 4
+specify existing encoded sequence (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-packedindex-trsuftab.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-trsuftab.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-trsuftab.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,88 @@
+'\" t
+.\" Title: gt-packedindex-trsuftab
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-PACKEDINDEX\-TRS" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-packedindex-trsuftab \- Build BWT packedindex for project [indexname]\&.
+.SH "SYNOPSIS"
+.sp
+gt packedindex trsuftab indexname
+.SH "OPTIONS"
+.PP
+\fB\-bsize\fR
+.RS 4
+specify size of blocks (default: 8)
+.RE
+.PP
+\fB\-blbuck\fR
+.RS 4
+specify number of blocks per bucket (default: 8)
+.RE
+.PP
+\fB\-locfreq\fR
+.RS 4
+specify the locate frequency parameter i means that each i\-th position of input string is stored 0 ⇒ no locate information (default: 16)
+.RE
+.PP
+\fB\-locbitmap\fR
+.RS 4
+marked/unmarked positions for locate are stored as bitmaps this gives faster location of hits but increases the index by 1 bit per symbol (default: yes)
+.RE
+.PP
+\fB\-sprank\fR
+.RS 4
+build rank table for special symbols this produces an index which can be used to regenerate the original sequence but increases the memory used during index creation (default: no)
+.RE
+.PP
+\fB\-sprankilog\fR
+.RS 4
+specify the interval of rank sampling as log value parameter i means that each 2^i\-th position of source is sampled for rank undefined ⇒ chooses default of log(log(sequence length)) (default: undefined)
+.RE
+.PP
+\fB\-ctxilog\fR
+.RS 4
+specify the interval of context sampling as log value parameter i means that each 2^i\-th position of source is sampled for rank \-1 ⇒ chooses default of log(log(sequence length)) \-2 ⇒ generates no map (default: \-2)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+print verbose progress information (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-packedindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,55 @@
+'\" t
+.\" Title: gt-packedindex
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-PACKEDINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-packedindex \- Call packed index tool with name index_tool and pass argument(s) to it\&.
+.SH "SYNOPSIS"
+.sp
+gt packedindex [option \&...] index_tool [argument \&...]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Tools:
+.sp
+chkintegrity chksearch mkctxmap mkindex trsuftab
+.sp
+For detailed information, please refer to the manual of packedindex\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-prebwt.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-prebwt.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-prebwt.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,58 @@
+'\" t
+.\" Title: gt-prebwt
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-PREBWT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-prebwt \- Precompute bwt\-bounds for some prefix length\&.
+.SH "SYNOPSIS"
+.sp
+gt prebwt [options] \-pck indexname
+.SH "OPTIONS"
+.PP
+\fB\-pck\fR
+.RS 4
+Specify index (packed index) (default: undefined)
+.RE
+.PP
+\fB\-maxdepth\fR
+.RS 4
+specify maximum depth (value > 0) (default: 0)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-readjoiner-assembly.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner-assembly.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner-assembly.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-readjoiner-assembly
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-READJOINER\-ASSE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-readjoiner-assembly \- Construct string graph and output contigs\&.
+.SH "SYNOPSIS"
+.sp
+gt readjoiner assembly [option \&...]
+.SH "OPTIONS"
+.PP
+\fB\-readset\fR
+.RS 4
+specify the readset name (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+suppress standard output messages (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-readjoiner-overlap.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner-overlap.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner-overlap.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,82 @@
+'\" t
+.\" Title: gt-readjoiner-overlap
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-READJOINER\-OVER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-readjoiner-overlap \- Compute suffix prefix matches from encoded sequence\&.
+.SH "SYNOPSIS"
+.sp
+gt readjoiner overlap [option \&...] [file]
+.SH "OPTIONS"
+.PP
+\fB\-readset\fR
+.RS 4
+specify the readset name (default: undefined)
+.RE
+.PP
+\fB\-l\fR
+.RS 4
+specify the minimum SPM length (default: 0)
+.RE
+.PP
+\fB\-parts\fR
+.RS 4
+specify the number of parts (default: 0)
+.RE
+.PP
+\fB\-memlimit\fR
+.RS 4
+specify maximal amount of memory to be used during index construction (in bytes, the keywords
+\fIMB\fR
+and
+\fIGB\fR
+are allowed) (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+suppress standard output messages (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-readjoiner-prefilter.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner-prefilter.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner-prefilter.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-readjoiner-prefilter
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-READJOINER\-PREF" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-readjoiner-prefilter \- Remove contained reads and reads containing ambiguity codes in given sequence_file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt readjoiner prefilter [option \&...]
+.SH "OPTIONS"
+.PP
+\fB\-readset\fR
+.RS 4
+specify the readset name (default: filename of first input sequence_file)
+.RE
+.PP
+\fB\-db\fR
+.RS 4
+specify the name of the input files (Fasta format); mate pairs and paired reads sets may be specified using the notation file1:file2:insertlength
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+suppress standard output messages (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-readjoiner.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,53 @@
+'\" t
+.\" Title: gt-readjoiner
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-READJOINER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-readjoiner \- String graph based sequencing reads assembler\&.
+.SH "SYNOPSIS"
+.sp
+gt readjoiner [option \&...] tool [argument \&...]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Tools:
+.sp
+assembly overlap prefilter
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-repfind.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-repfind.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-repfind.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-repfind
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-REPFIND" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-repfind \- Compute maximal repeats\&.
+.SH "SYNOPSIS"
+.sp
+gt repfind [options] \-ii indexname
+.SH "OPTIONS"
+.PP
+\fB\-l\fR
+.RS 4
+Specify minimum length of repeats (default: 20)
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Compute maximal forward repeats (default: yes)
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+Compute maximal reverse matches (default: no)
+.RE
+.PP
+\fB\-scan\fR
+.RS 4
+scan index rather than mapping it to main memory (default: no)
+.RE
+.PP
+\fB\-ii\fR
+.RS 4
+Specify input index (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-scriptfilter.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-scriptfilter.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-scriptfilter.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-scriptfilter
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SCRIPTFILTER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-scriptfilter \- Get info about and validate Lua script filters\&.
+.SH "SYNOPSIS"
+.sp
+gt scriptfilter [option \&...] [script file(s)]
+.SH "OPTIONS"
+.PP
+\fB\-showinfo\fR
+.RS 4
+show information about filter (default: yes)
+.RE
+.PP
+\fB\-validate\fR
+.RS 4
+validate filter function (default: yes)
+.RE
+.PP
+\fB\-oneline\fR
+.RS 4
+show compact information on one line (default: no)
+.RE
+.PP
+\fB\-scriptname\fR
+.RS 4
+show script name (default: yes)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-select.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-select.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-select.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,211 @@
+'\" t
+.\" Title: gt-select
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SELECT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-select \- Select certain features (specified by the used options) from given GFF3 file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt select [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-seqid\fR
+.RS 4
+select feature with the given sequence ID (all comments are selected)\&. (default: undefined)
+.RE
+.PP
+\fB\-source\fR
+.RS 4
+select feature with the given source (the source is column 2 in regular GFF3 lines) (default: undefined)
+.RE
+.PP
+\fB\-contain\fR
+.RS 4
+select all features which are contained in the given range (default: undefined)
+.RE
+.PP
+\fB\-overlap\fR
+.RS 4
+select all features which do overlap with the given range (default: undefined)
+.RE
+.PP
+\fB\-strand\fR
+.RS 4
+select all top\-level features(i\&.e\&., features without parents) whose strand equals the given one (must be one of
+\fI+\-\&.?\fR) (default: undefined)
+.RE
+.PP
+\fB\-targetstrand\fR
+.RS 4
+select all top\-level features (i\&.e\&., features without parents) which have exactly one target attribute whose strand equals the given one (must be one of
+\fI+\-\&.?\fR) (default: undefined)
+.RE
+.PP
+\fB\-targetbest\fR
+.RS 4
+if multiple top\-level features (i\&.e\&., features without parents) with exactly one target attribute have the same target_id, keep only the feature with the best score\&. If \-targetstrand is used at the same time, this option is applied after \-targetstrand\&. Memory consumption is proportional to the input file size(s)\&. (default: no)
+.RE
+.PP
+\fB\-hascds\fR
+.RS 4
+select all top\-level features which do have a CDS child (default: no)
+.RE
+.PP
+\fB\-maxgenelength\fR
+.RS 4
+select genes up to the given maximum length (default: undefined)
+.RE
+.PP
+\fB\-maxgenenum\fR
+.RS 4
+select the first genes up to the given maximum number (default: undefined)
+.RE
+.PP
+\fB\-mingenescore\fR
+.RS 4
+select genes with the given minimum score (default: undefined)
+.RE
+.PP
+\fB\-maxgenescore\fR
+.RS 4
+select genes with the given maximum score (default: undefined)
+.RE
+.PP
+\fB\-minaveragessp\fR
+.RS 4
+set the minimum average splice site probability (default: undefined)
+.RE
+.PP
+\fB\-rule_files\fR
+.RS 4
+specify Lua files to be used for selection
+.RE
+.PP
+\fB\-rule_logic\fR
+.RS 4
+select how multiple Lua files should be combined choose from AND|OR (default: AND)
+.RE
+.PP
+\fB\-dropped_file\fR
+.RS 4
+save non\-selected features to file (default: undefined)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+File format for option \-rule_files:
+.sp
+The files supplied to option \-rule_files define a function for filtering by user given criteria (see example below):
+.sp
+function filter(gn) target = "exon" gfi = gt\&.feature_node_iterator_new(gn)
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+curnode = gfi:next()
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+while not(curnode == nil) do
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+ if (curnode:get_type() == target) then
+ return false
+ end
+ curnode = gfi:next()
+end
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+ return true
+end
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+The above function iterates over all children of \fIgn\fR and checks whether there is a node of type \fIexon\fR\&. If there is such a node the function returns \fIfalse\fR, indicating that the parent node \fIgn\fR will not be sorted out\&.
+.sp
+NOTE: The function must be named \fIfilter\fR and must return \fIfalse\fR, indicating that the node survived the filtering process\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seq.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seq.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,103 @@
+'\" t
+.\" Title: gt-seq
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seq \- Parse the given sequence file(s) and construct the corresponding index files\&.
+.SH "SYNOPSIS"
+.sp
+gt seq [option \&...] sequence_file [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-recreate\fR
+.RS 4
+recreate index files, even if they exist already (default: no)
+.RE
+.PP
+\fB\-showfasta\fR
+.RS 4
+show all sequences (in FASTA format) (default: no)
+.RE
+.PP
+\fB\-showseqnum\fR
+.RS 4
+show sequence with given number (in FASTA format) (default: undefined)
+.RE
+.PP
+\fB\-gc\-content\fR
+.RS 4
+print GC\-content (for DNA files) (default: no)
+.RE
+.PP
+\fB\-stat\fR
+.RS 4
+show sequence statistics (default: no)
+.RE
+.PP
+\fB\-seqlengthdistri\fR
+.RS 4
+show sequence length distribution (default: no)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seqfilter.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqfilter.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqfilter.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,88 @@
+'\" t
+.\" Title: gt-seqfilter
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQFILTER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seqfilter \- Filter the given sequence_file(s) and show the results on stdout\&.
+.SH "SYNOPSIS"
+.sp
+gt seqfilter [option \&...] [sequence_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-minlength\fR
+.RS 4
+set minimum length a sequence must have to pass the filter (default: undefined)
+.RE
+.PP
+\fB\-maxlength\fR
+.RS 4
+set maximum length a sequence can have to pass the filter (default: undefined)
+.RE
+.PP
+\fB\-maxseqnum\fR
+.RS 4
+set the maximum number of sequences which can pass the filter (default: undefined)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seqids.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqids.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqids.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,48 @@
+'\" t
+.\" Title: gt-seqids
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQIDS" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seqids \- Show sequence IDs from annotation file\&.
+.SH "SYNOPSIS"
+.sp
+gt seqids [GFF3_file]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seqmutate.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqmutate.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqmutate.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: gt-seqmutate
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQMUTATE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seqmutate \- Mutate the sequences of the given sequence file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt seqmutate [option \&...] [sequence_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-rate\fR
+.RS 4
+set the mutation rate (default: 1)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+For each position in the given sequences it is randomly determined with probability (mutation rate / 100) if the given position is mutated\&. If so, in 80% of the cases a substitution is performed, in 10% an insertion, and in 10% a deletion, respectively\&. For substitution and insertion events, the nucleotide is generated randomly without regard to the original nucleotide\&. That is, resubstitutions are possible\&. This procedure equals the one described on page 1867 of the following paper
+.sp
+T\&.D\&. Wu and C\&.K\&. Watanabe\&. GMAP: a genomic mapping and alignment program for mRNA and EST sequences\&. Bioinformatics, 21(9):1859\-1875, 2005\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seqorder.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqorder.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqorder.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-seqorder
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQORDER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seqorder \- Output sequences as MultiFasta in specified order\&.
+.SH "SYNOPSIS"
+.sp
+gt seqorder (\-invert|\-sort|\-revsort|\-shuffle) encseq
+.SH "OPTIONS"
+.PP
+\fB\-invert\fR
+.RS 4
+invert order of sequences (default: no)
+.RE
+.PP
+\fB\-sort\fR
+.RS 4
+sort sequences lexicographically (default: no)
+.RE
+.PP
+\fB\-revsort\fR
+.RS 4
+sort sequences in reverse lexicographic order (default: no)
+.RE
+.PP
+\fB\-shuffle\fR
+.RS 4
+shuffle sequences pseudo\-randomly (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seqstat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqstat.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqstat.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: gt-seqstat
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQSTAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seqstat \- Calculate statistics for fasta file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt seqstat [options] file [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-distlen\fR
+.RS 4
+show distribution of sequence length (default: no)
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+bucket size for distlen option (default: 100)
+.RE
+.PP
+\fB\-binary\fR
+.RS 4
+use a binary format for distlen output output filename: <first_input_filename>\&.distlen bucketsize: 1 (default: no)
+.RE
+.PP
+\fB\-contigs\fR
+.RS 4
+summary of contigs set statistics (default: no)
+.RE
+.PP
+\fB\-genome\fR
+.RS 4
+set genome length for NG50/NG80 calculation (default: 0)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seqtransform.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqtransform.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqtransform.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-seqtransform
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQTRANSFORM" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seqtransform \- Perform simple transformations on the given sequence file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt seqtransform [option \&...] [sequence_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-addstopaminos\fR
+.RS 4
+append stop amino acids (\fI*\fR) to given protein sequences, if not already present (default: no)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-seqtranslate.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqtranslate.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqtranslate.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: gt-seqtranslate
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQTRANSLATE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-seqtranslate \- Translates a nucleotide sequence into a protein sequence\&.
+.SH "SYNOPSIS"
+.sp
+gt seqtranslate [option \&...] [files]
+.SH "OPTIONS"
+.PP
+\fB\-reverse\fR
+.RS 4
+also translate reverse complements (default: yes)
+.RE
+.PP
+\fB\-fastawidth\fR
+.RS 4
+width of the FASTA output (default: 60)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-sequniq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-sequniq.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-sequniq.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: gt-sequniq
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SEQUNIQ" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-sequniq \- Filter out repeated sequences in given in given sequence_file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt sequniq [option \&...] sequence_file [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-rev\fR
+.RS 4
+filter out also sequences whose reverse complement is identical to a sequence already output (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-shredder.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-shredder.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-shredder.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,114 @@
+'\" t
+.\" Title: gt-shredder
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SHREDDER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-shredder \- Shredder sequence file(s) into consecutive pieces of random length\&.
+.SH "SYNOPSIS"
+.sp
+gt shredder [option \&...] [sequence_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-coverage\fR
+.RS 4
+set the number of times the sequence_file is shreddered (default: 1)
+.RE
+.PP
+\fB\-minlength\fR
+.RS 4
+set the minimum length of the shreddered fragments (default: 300)
+.RE
+.PP
+\fB\-maxlength\fR
+.RS 4
+set the maximum length of the shreddered fragments (default: 700)
+.RE
+.PP
+\fB\-overlap\fR
+.RS 4
+set the overlap between consecutive pieces (default: 0)
+.RE
+.PP
+\fB\-sample\fR
+.RS 4
+take samples of the generated sequences pieces with the given probability (default: 1\&.00)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Each sequence given in sequence_file is shreddered into consecutive pieces of random length (between \-minlength and \-maxlength) until it is consumed\&. By this means the last shreddered fragment of a given sequence can be shorter than the argument to option \-minlength\&. To get rid of such fragments use gt seqfilter (see example below)\&.
+.SH "EXAMPLES:"
+.sp
+Shredder a given BAC
+.sp
+$ gt shredder U89959_genomic\&.fas > fragments\&.fas
+.sp
+Shredder an EST collection into pieces between 50 and 100 bp and get rid of all (terminal) fragments shorter than 50 bp
+.sp
+$ gt shredder \-minlength 50 \-maxlength 100 U89959_ests\&.fas \e | gt seqfilter \-minlength 50 \- > fragments\&.fas # 130 out of 1260 sequences have been removed (10\&.317%)
+.sp
+Shredder an EST collection and show only random 10% of the resulting fragments
+.sp
+$ gt shredder \-sample 0\&.1 U89959_ests\&.fas
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-shulengthdist.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-shulengthdist.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-shulengthdist.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,63 @@
+'\" t
+.\" Title: gt-shulengthdist
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SHULENGTHDIST" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-shulengthdist \- Compute distribution of pairwise shustring lengths\&.
+.SH "SYNOPSIS"
+.sp
+gt shulengthdist [options] \-ii indexname
+.SH "OPTIONS"
+.PP
+\fB\-ii\fR
+.RS 4
+Specify input index (default: undefined)
+.RE
+.PP
+\fB\-scan\fR
+.RS 4
+scan index rather than mapping it to main memory (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-simreads.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-simreads.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-simreads.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,118 @@
+'\" t
+.\" Title: gt-simreads
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SIMREADS" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-simreads \- Simulate sequencing reads from random positions in the input sequence(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt simreads [option \&...] <encseq>
+.SH "OPTIONS"
+.PP
+\fB\-num\fR
+.RS 4
+desired number of reads (default: undefined)
+.RE
+.PP
+\fB\-coverage\fR
+.RS 4
+desired coverage of the reads (default: undefined)
+.RE
+.PP
+\fB\-len\fR
+.RS 4
+fixed read length (default: undefined)
+.RE
+.PP
+\fB\-minlen\fR
+.RS 4
+minimal read length (default: undefined)
+.RE
+.PP
+\fB\-maxlen\fR
+.RS 4
+maximal read length (default: undefined)
+.RE
+.PP
+\fB\-distlen\fR
+.RS 4
+use read length distribution file (in the output format of the seqstat tool) (default: undefined)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+show a progress bar (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-ss\fR
+.RS 4
+simulate reads in forward direction only (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gonnella at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-sketch.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-sketch.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-sketch.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,113 @@
+'\" t
+.\" Title: gt-sketch
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SKETCH" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-sketch \- Create graphical representation of GFF3 annotation files\&.
+.SH "SYNOPSIS"
+.sp
+gt sketch [option \&...] image_file [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-pipe\fR
+.RS 4
+use pipe mode (i\&.e\&., show all gff3 features on stdout) (default: no)
+.RE
+.PP
+\fB\-flattenfiles\fR
+.RS 4
+do not group tracks by source file name and remove file names from track description (default: no)
+.RE
+.PP
+\fB\-seqid\fR
+.RS 4
+sequence region identifier (default: first one in file)
+.RE
+.PP
+\fB\-start\fR
+.RS 4
+start position (default: first region start)
+.RE
+.PP
+\fB\-end\fR
+.RS 4
+end position (default: last region end)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+target image width (in pixel) (default: 800)
+.RE
+.PP
+\fB\-style\fR
+.RS 4
+style file to use (default: bin/\&.\&./gtdata/sketch/default\&.style)
+.RE
+.PP
+\fB\-format\fR
+.RS 4
+output graphics format choose from png|pdf|svg|ps (default: png)
+.RE
+.PP
+\fB\-input\fR
+.RS 4
+input data format choose from gff|bed|gtf (default: gff)
+.RE
+.PP
+\fB\-addintrons\fR
+.RS 4
+add intron features between existing exon features (before drawing) (default: no)
+.RE
+.PP
+\fB\-unsafe\fR
+.RS 4
+enable unsafe mode for style file (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-sketch_page.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-sketch_page.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-sketch_page.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,100 @@
+'\" t
+.\" Title: gt-sketch_page
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SKETCH_PAGE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-sketch_page \- Draw a multi\-page PDF/PS representation of an annotation file\&.
+.SH "SYNOPSIS"
+.sp
+gt sketch_page outfile annotationfile
+.SH "OPTIONS"
+.PP
+\fB\-seqid\fR
+.RS 4
+sequence region to draw (default: first in file)
+.RE
+.PP
+\fB\-text\fR
+.RS 4
+text to show in header (default: file name)
+.RE
+.PP
+\fB\-fontsize\fR
+.RS 4
+header and footer font size (in points) (default: 10\&.00)
+.RE
+.PP
+\fB\-range\fR
+.RS 4
+range to draw (e\&.g\&. 100 10000) (default: full range)
+.RE
+.PP
+\fB\-linewidth\fR
+.RS 4
+base width of a single repeated unit (default: 2000)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+page width in millimeters
+.\" default: DIN A4default: DIN A4 (default: 210\&.00)
+.RE
+.PP
+\fB\-height\fR
+.RS 4
+page height in millimeters
+.\" default: DIN A4default: DIN A4 (default: 297\&.00)
+.RE
+.PP
+\fB\-format\fR
+.RS 4
+output format choose from: pdf|ps (default: pdf)
+.RE
+.PP
+\fB\-style\fR
+.RS 4
+style file to use (default: gtdata/sketch/default\&.style)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-splicesiteinfo.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-splicesiteinfo.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-splicesiteinfo.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,113 @@
+'\" t
+.\" Title: gt-splicesiteinfo
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SPLICESITEINFO" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-splicesiteinfo \- Show information about splice sites given in GFF3 files\&.
+.SH "SYNOPSIS"
+.sp
+gt splicesiteinfo [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-seqfile\fR
+.RS 4
+set the sequence file from which to extract the features (default: undefined)
+.RE
+.PP
+\fB\-seqfiles\fR
+.RS 4
+set the sequence files from which to extract the features use
+\fI\-\-\fR
+to terminate the list of sequence files
+.RE
+.PP
+\fB\-matchdesc\fR
+.RS 4
+match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) (default: no)
+.RE
+.PP
+\fB\-usedesc\fR
+.RS 4
+use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries\&. If a description contains a sequence range (e\&.g\&., III:1000001\&.\&.2000000), the first part is used as sequence ID (\fIIII\fR) and the first range position as offset (\fI1000001\fR) (default: no)
+.RE
+.PP
+\fB\-regionmapping\fR
+.RS 4
+set file containing sequence\-region to sequence file mapping (default: undefined)
+.RE
+.PP
+\fB\-addintrons\fR
+.RS 4
+add intron features between existing exon features (before computing the information to be shown) (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+File format for option \-regionmapping:
+.sp
+The file supplied to option \-regionmapping defines a \(lqmapping\(rq\&. A mapping maps the sequence\-regions given in the GFF3_file to a sequence file containing the corresponding sequence\&. Mappings can be defined in one of the following two forms:
+.sp
+mapping = { chr1 = "hs_ref_chr1\&.fa\&.gz", chr2 = "hs_ref_chr2\&.fa\&.gz" }
+.sp
+or
+.sp
+function mapping(sequence_region) return "hs_ref_"\&.\&.sequence_region\&.\&."\&.fa\&.gz" end
+.sp
+The first form defines a Lua (http://www\&.lua\&.org/) table named \(lqmapping\(rq which maps each sequence region to the corresponding sequence file\&. The second one defines a Lua function \(lqmapping\(rq, which has to return the sequence file name when it is called with the sequence_region as argument\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-splitfasta.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-splitfasta.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-splitfasta.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-splitfasta
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SPLITFASTA" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-splitfasta \- Split the supplied fasta file\&.
+.SH "SYNOPSIS"
+.sp
+gt splitfasta [option \&...] fastafile
+.SH "OPTIONS"
+.PP
+\fB\-numfiles\fR
+.RS 4
+set the number of target files (default: 0)
+.RE
+.PP
+\fB\-targetsize\fR
+.RS 4
+set the target file size in MB (default: 50)
+.RE
+.PP
+\fB\-splitdesc\fR
+.RS 4
+put every fasta entry in a separate file named by its description in the given directory (default: undefined)
+.RE
+.PP
+\fB\-width\fR
+.RS 4
+set output width for FASTA sequence printing (0 disables formatting) (default: 0)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-stat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-stat.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-stat.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,113 @@
+'\" t
+.\" Title: gt-stat
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-STAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-stat \- Show statistics about features contained in GFF3 files\&.
+.SH "SYNOPSIS"
+.sp
+gt stat [option \&...] [GFF3_file \&...]
+.SH "OPTIONS"
+.PP
+\fB\-genelengthdistri\fR
+.RS 4
+show gene length distribution (default: no)
+.RE
+.PP
+\fB\-genescoredistri\fR
+.RS 4
+show gene score distribution (default: no)
+.RE
+.PP
+\fB\-exonlengthdistri\fR
+.RS 4
+show exon length distribution (default: no)
+.RE
+.PP
+\fB\-exonnumberdistri\fR
+.RS 4
+show exon number distribution (default: no)
+.RE
+.PP
+\fB\-intronlengthdistri\fR
+.RS 4
+show intron length distribution (default: no)
+.RE
+.PP
+\fB\-cdslengthdistri\fR
+.RS 4
+show CDS length distribution (measured in amino acids) (default: no)
+.RE
+.PP
+\fB\-source\fR
+.RS 4
+show the set of used source tags (column 2 in regular GFF3 lines) (default: no)
+.RE
+.PP
+\fB\-addintrons\fR
+.RS 4
+add intron features between existing exon features (before computing stats) (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-suffixerator.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-suffixerator.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-suffixerator.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,182 @@
+'\" t
+.\" Title: gt-suffixerator
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-SUFFIXERATOR" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-suffixerator \- Compute enhanced suffix array\&.
+.SH "SYNOPSIS"
+.sp
+gt suffixerator [option \&...] (\-db file [\&...] | \-ii index)
+.SH "OPTIONS"
+.PP
+\fB\-ssp\fR
+.RS 4
+output sequence separator positions to file (default: yes)
+.RE
+.PP
+\fB\-des\fR
+.RS 4
+output sequence descriptions to file (default: yes)
+.RE
+.PP
+\fB\-sds\fR
+.RS 4
+output sequence description separator positions to file (default: yes)
+.RE
+.PP
+\fB\-md5\fR
+.RS 4
+output MD5 sums to file (default: yes)
+.RE
+.PP
+\fB\-sat\fR
+.RS 4
+specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
+.RE
+.PP
+\fB\-dna\fR
+.RS 4
+input is DNA sequence (default: no)
+.RE
+.PP
+\fB\-protein\fR
+.RS 4
+input is protein sequence (default: no)
+.RE
+.PP
+\fB\-indexname\fR
+.RS 4
+specify name for index to be generated (default: undefined)
+.RE
+.PP
+\fB\-db\fR
+.RS 4
+specify database files
+.RE
+.PP
+\fB\-smap\fR
+.RS 4
+specify file containing a symbol mapping (default: undefined)
+.RE
+.PP
+\fB\-lossless\fR
+.RS 4
+allow lossless original sequence retrieval (default: no)
+.RE
+.PP
+\fB\-mirrored\fR
+.RS 4
+virtually append the reverse complement of each sequence (default: no)
+.RE
+.PP
+\fB\-pl\fR
+.RS 4
+specify prefix length for bucket sort recommendation: use without argument; then a reasonable prefix length is automatically determined (default: 0)
+.RE
+.PP
+\fB\-dc\fR
+.RS 4
+specify difference cover value (default: 0)
+.RE
+.PP
+\fB\-kys\fR
+.RS 4
+output/sort according to keys of the form |key| in fasta header (default: nosort)
+.RE
+.PP
+\fB\-suf\fR
+.RS 4
+output suffix array (suftab) to file (default: no)
+.RE
+.PP
+\fB\-lcp\fR
+.RS 4
+output lcp table (lcptab) to file (default: no)
+.RE
+.PP
+\fB\-bwt\fR
+.RS 4
+output Burrows\-Wheeler Transformation (bwttab) to file (default: no)
+.RE
+.PP
+\fB\-bck\fR
+.RS 4
+output bucket table to file (default: no)
+.RE
+.PP
+\fB\-spmopt\fR
+.RS 4
+optimize esa\-construction for suffix\-prefix matching (default: 0)
+.RE
+.PP
+\fB\-memlimit\fR
+.RS 4
+specify maximal amount of memory to be used during index construction (in bytes, the keywords
+\fIMB\fR
+and
+\fIGB\fR
+are allowed) (default: undefined)
+.RE
+.PP
+\fB\-dir\fR
+.RS 4
+specify reading direction (fwd, cpl, rev, rcl) (default: fwd)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-showprogress\fR
+.RS 4
+show a progress bar (default: no)
+.RE
+.PP
+\fB\-ii\fR
+.RS 4
+specify existing encoded sequence (default: undefined)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help for basic options and exit
+.RE
+.PP
+\fB\-help+\fR
+.RS 4
+display help for all options and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-tagerator.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tagerator.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-tagerator.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,108 @@
+'\" t
+.\" Title: gt-tagerator
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-TAGERATOR" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-tagerator \- Map short sequence tags in given index\&.
+.SH "SYNOPSIS"
+.sp
+gt tagerator [options] \-q tagfile [\-esa|\-pck] indexname
+.SH "OPTIONS"
+.PP
+\fB\-q\fR
+.RS 4
+Specify files containing the short sequence tags
+.RE
+.PP
+\fB\-e\fR
+.RS 4
+Specify the allowed number of differences (replacements/insertions/deletions) (default: \-1)
+.RE
+.PP
+\fB\-esa\fR
+.RS 4
+Specify index (enhanced suffix array) (default: undefined)
+.RE
+.PP
+\fB\-pck\fR
+.RS 4
+Specify index (packed index) (default: undefined)
+.RE
+.PP
+\fB\-nod\fR
+.RS 4
+Do not compute direct matches (default: no)
+.RE
+.PP
+\fB\-nop\fR
+.RS 4
+Do not compute palindromic matches (i\&.e\&. no reverse complemented matches\&.) (default: no)
+.RE
+.PP
+\fB\-best\fR
+.RS 4
+Compute only best matches, i\&.e\&. only for smallest edit distance with matches (default: no)
+.RE
+.PP
+\fB\-maxocc\fR
+.RS 4
+specify max number of match\-occurrences (default: 0)
+.RE
+.PP
+\fB\-skpp\fR
+.RS 4
+Skip prefix of pattern (only in pdiff mode) (default: no)
+.RE
+.PP
+\fB\-withwildcards\fR
+.RS 4
+output matches containing wildcard characters (e\&.g\&. N); only relevant for approximate matching (default: yes)
+.RE
+.PP
+\fB\-output\fR
+.RS 4
+use combination of the following keywords to specify output tagnum show ordinal number of tag tagseq show tag sequence dblength show length of match in database dbstartpos show start position of match in database abspos show absolute value of dbstartpos dbsequence show sequence of match strand show strand edist show edit distance tagstartpos show start position of match in tag (only for \-maxocc) taglength show length of match in tag (only for \-maxocc) tagsuffixseq show suffix tag involved in match (only for \-maxocc)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-tallymer-mkindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer-mkindex.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer-mkindex.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,93 @@
+'\" t
+.\" Title: gt-tallymer-mkindex
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-TALLYMER\-MKINDE" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-tallymer-mkindex \- Count and index k\-mers in the given enhanced suffix array for a fixed value of k\&.
+.SH "SYNOPSIS"
+.sp
+gt tallymer mkindex [options] \-esa suffixerator\-index [options]
+.SH "OPTIONS"
+.PP
+\fB\-esa\fR
+.RS 4
+specify suffixerator\-index (mandatory option) (default: undefined)
+.RE
+.PP
+\fB\-mersize\fR
+.RS 4
+Specify the mer size\&. (default: 20)
+.RE
+.PP
+\fB\-minocc\fR
+.RS 4
+Specify the minimum occurrence number for the mers to output/index (default: 0)
+.RE
+.PP
+\fB\-maxocc\fR
+.RS 4
+Specify the maximum occurrence number for the mers to output/index (default: 0)
+.RE
+.PP
+\fB\-pl\fR
+.RS 4
+specify prefix length for bucket boundary construction recommendation: use without argument; then a reasonable prefix length is automatically determined (default: 0)
+.RE
+.PP
+\fB\-indexname\fR
+.RS 4
+store the mers specified by options \-maxocc and \-minocc in an index (default: undefined)
+.RE
+.PP
+\fB\-counts\fR
+.RS 4
+store counts of the mers (default: no)
+.RE
+.PP
+\fB\-scan\fR
+.RS 4
+read enhanced suffix array sequentially instead of mapping it to memory (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-tallymer-occratio.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer-occratio.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer-occratio.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,88 @@
+'\" t
+.\" Title: gt-tallymer-occratio
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-TALLYMER\-OCCRAT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-tallymer-occratio \- Compute occurrence ratio for a set of sequences represented by an enhanced suffix array\&.
+.SH "SYNOPSIS"
+.sp
+gt tallymer occratio [options] \-esa suffixerator\-index [options]
+.SH "OPTIONS"
+.PP
+\fB\-esa\fR
+.RS 4
+specify suffixerator\-index (mandatory option) (default: undefined)
+.RE
+.PP
+\fB\-minmersize\fR
+.RS 4
+specify minimum mer size for which to compute the occurrence distribution (default: 0)
+.RE
+.PP
+\fB\-maxmersize\fR
+.RS 4
+specify maximum mer size for which to compute the occurrence distribution (default: 0)
+.RE
+.PP
+\fB\-step\fR
+.RS 4
+specify step size when specifying mer sizes (default: 1)
+.RE
+.PP
+\fB\-mersizes\fR
+.RS 4
+specify mer sizes as non\-empty sequence of non decreasing positive integers
+.RE
+.PP
+\fB\-output\fR
+.RS 4
+use combination of the following keywords: unique nonunique nonuniquemulti relative total to specify kind of output
+.RE
+.PP
+\fB\-scan\fR
+.RS 4
+read suffixerator\-index sequentially instead of mapping it to memory (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-tallymer-search.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer-search.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer-search.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: gt-tallymer-search
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-TALLYMER\-SEARCH" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-tallymer-search \- Search a set of k\-mers in an index constructed by "gt tyr mkindex"\&.
+.SH "SYNOPSIS"
+.sp
+gt tallymer search [options] \-tyr tallymer\-index \-q queryfile0 [queryfile1\&.\&.] [options]
+.SH "OPTIONS"
+.PP
+\fB\-tyr\fR
+.RS 4
+specify tallymer\-index (default: undefined)
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+specify query file names
+.RE
+.PP
+\fB\-strand\fR
+.RS 4
+specify the strand to be searched: use f (for forward strand) or p (for reverse complemented strand) or fp (for both); default is f (default: f)
+.RE
+.PP
+\fB\-output\fR
+.RS 4
+specify output flags (qseqnum, qpos, counts, sequence)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-tallymer.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,55 @@
+'\" t
+.\" Title: gt-tallymer
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-TALLYMER" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-tallymer \- Call tallymer tool with name tallymer_tool and pass argument(s) to it\&.
+.SH "SYNOPSIS"
+.sp
+gt tallymer [option \&...] tallymer_tool [argument \&...]
+.SH "OPTIONS"
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Tools:
+.sp
+mkindex occratio search
+.sp
+For detailed information, please refer to the manual of tallymer\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-uniq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-uniq.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-uniq.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,82 @@
+'\" t
+.\" Title: gt-uniq
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-UNIQ" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-uniq \- Filter out repeated feature node graphs in a sorted GFF3 file\&.
+.SH "SYNOPSIS"
+.sp
+gt uniq [option \&...] [GFF3_file]
+.SH "OPTIONS"
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+A depth\-first traversal of a feature node graph starts at the top\-level feature node (or pseudo\-node) and explores as far along each branch as possible before backtracking\&. Let\(cqs assume that the feature nodes are stored in a list in the order of their traversal (called the \(lqfeature node list\(rq)\&.
+.sp
+Two feature node graphs are considered to be repeated if their feature node list (from the depth\-first traversal) have the same length and each feature node pair (from both lists at the same position) is \(lqsimilar\(rq\&.
+.sp
+Two feature nodes are \(lqsimilar\(rq, if they have the same sequence ID, feature type, range, strand, and phase\&.
+.sp
+For such a repeated feature node graph the one with the higher score (of the top\-level feature) is kept\&. If only one of the feature node graphs has a defined score, this one is kept\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt-uniquesub.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-uniquesub.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-uniquesub.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,86 @@
+'\" t
+.\" Title: gt-uniquesub
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-UNIQUESUB" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-uniquesub \- Compute length of minumum unique prefixes\&.
+.SH "SYNOPSIS"
+.sp
+gt uniquesub [options \&...] \-query queryfile [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-fmi\fR
+.RS 4
+specify fmindex (default: undefined)
+.RE
+.PP
+\fB\-esa\fR
+.RS 4
+specify suffix array (default: undefined)
+.RE
+.PP
+\fB\-pck\fR
+.RS 4
+specify packed index (default: undefined)
+.RE
+.PP
+\fB\-query\fR
+.RS 4
+specify queryfiles
+.RE
+.PP
+\fB\-min\fR
+.RS 4
+only output length if >= given minimum length (default: 0)
+.RE
+.PP
+\fB\-max\fR
+.RS 4
+only output length if ⇐ given maximum length (default: 0)
+.RE
+.PP
+\fB\-output\fR
+.RS 4
+set output flags (sequence, querypos)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+For detailed information, please refer to the manual of uniquesub\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <kurtz at zbh\&.uni\-hamburg\&.de>\&.
Added: trunk/packages/genometools/trunk/debian/man/gt.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt.1 2012-07-11 12:17:17 UTC (rev 11733)
@@ -0,0 +1,72 @@
+'\" t
+.\" Title: gt
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 07/11/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT" "1" "07/11/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt \- The GenomeTools (gt) genome analysis system (http://genometools\&.org)\&.
+.SH "SYNOPSIS"
+.sp
+gt [option \&...] [tool | script] [argument \&...]
+.SH "OPTIONS"
+.PP
+\fB\-i\fR
+.RS 4
+enter interactive mode after executing
+\fItool\fR
+or
+\fIscript\fR
+.RE
+.PP
+\fB\-test\fR
+.RS 4
+perform unit tests and exit
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Tools:
+.sp
+bed_to_gff3 cds chain2dim chseqids clean compreads congruence convertseq csa dupfeat encseq encseq2spm eval extractfeat extractseq featureindex fingerprint genomediff gff3 gff3_to_gtf gff3validator gtf_to_gff3 id_to_md5 interfeat ltrclustering ltrdigest ltrharvest matchtool matstat md5_to_id merge mergefeat mgth mkfeatureindex mkfmindex mmapandread orffinder packedindex prebwt readjoiner repfind scriptfilter select seq seqfilter seqids seqmutate seqorder seqstat seqtransform seqtranslate sequniq shredder shulengthdist simreads sketch sketch_page splicesiteinfo splitfasta stat suffixerator tagerator tallymer uniq uniquesub
+.sp
+Set the environment variable GT_MEM_BOOKKEEPING=on to enable memory bookkeeping (e\&.g\&., like this: env GT_MEM_BOOKKEEPING=on gt)\&.
+.sp
+Set the environment variable GT_ENV_OPTIONS=\-spacepeak to show a spacepeak after program run\&. Set the environment variable GT_ENV_OPTIONS=\-showtime to show processing times for some program parts if implemented\&.
+.sp
+Combinations are possible\&. Running the \(oqgt\(cq binary with GT_ENV_OPTIONS=\-help shows all possible \(lqenvironment options\(rq)
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
More information about the debian-med-commit
mailing list