[med-svn] r12324 - trunk/packages/genometools/trunk/debian/man
Sascha Steinbiss
sascha-guest at alioth.debian.org
Sun Oct 7 17:33:05 UTC 2012
Author: sascha-guest
Date: 2012-10-07 17:33:05 +0000 (Sun, 07 Oct 2012)
New Revision: 12324
Added:
trunk/packages/genometools/trunk/debian/man/gt-encseq-bench.1
trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1
trunk/packages/genometools/trunk/debian/man/gt-hop.1
Modified:
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:
update man pages
Modified: trunk/packages/genometools/trunk/debian/man/gt-bed_to_gff3.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-bed_to_gff3.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-bed_to_gff3.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" 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
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-BED_TO_GFF3" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-BED_TO_GFF3" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-cds.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-cds.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-cds.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-cds
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-CDS" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-CDS" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-chain2dim.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-chain2dim.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-chain2dim.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-chain2dim
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-CHAIN2DIM" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-CHAIN2DIM" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -41,17 +41,105 @@
.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
+perform global chaining
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+optional parameter gc switches on gap costs (according to L1\-model)
.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+optional parameter ov means that overlaps between matches are allowed
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+optional parameter all means that all optimal chains are processed
+.RE
+.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\&.
+perform local chaining compute local chains (according to L1\-model)\&.
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+If no parameter is given, compute local chains with maximums score\&.
.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+If parameter is given, this must be a positive number optionally followed by the character b or p\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+If only the number, say k, is given, this is the minimum score of the chains output\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+If a number is followed by character b, then output all chains with the largest k scores\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+If a number is followed by character p, then output all chains with scores at most k percent away from the best score\&.
+.RE
+.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)
+specify weight factor > 0\&.0 to obtain score of a fragment requires one of the options \-local const \-global gc \-global ov (default: 1\&.00)
.RE
.PP
\fB\-maxgap\fR
Modified: trunk/packages/genometools/trunk/debian/man/gt-chseqids.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-chseqids.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-chseqids.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-chseqids
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-CHSEQIDS" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-CHSEQIDS" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -81,7 +81,7 @@
.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\&.
+When this example is used, all sequence ids \(lqchr1\(rq will be changed to \(lqseq1\*(Aq \*(Aq and all sequence ids ``chr2\(rq to \(lqseq2\(rq\&.
.SH "AUTHOR"
.sp
Report bugs to <gt\-users at genometools\&.org>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-clean.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-clean.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-clean.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-clean
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-CLEAN" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-CLEAN" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-compreads-compress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-compress.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-compress.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-compreads-compress
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-COMPREADS\-COMPR" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-COMPREADS\-COMPR" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-compreads-decompress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-decompress.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-decompress.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-compreads-decompress
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-COMPREADS\-DECOM" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-COMPREADS\-DECOM" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-compreads-refcompress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-refcompress.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-refcompress.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-compreads-refcompress
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-COMPREADS\-REFCO" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-COMPREADS\-REFCO" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-compreads-refdecompress.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads-refdecompress.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads-refdecompress.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-compreads-refdecompress
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-COMPREADS\-REFDE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-COMPREADS\-REFDE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-compreads.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-compreads.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-compreads.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-compreads
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-COMPREADS" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-COMPREADS" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-congruence-spacedseed.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-congruence-spacedseed.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-congruence-spacedseed.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-congruence-spacedseed
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-CONGRUENCE\-SPAC" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-CONGRUENCE\-SPAC" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-congruence.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-congruence.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-congruence.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-congruence
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-CONGRUENCE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-CONGRUENCE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-convertseq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-convertseq.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-convertseq.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-convertseq
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-CONVERTSEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-CONVERTSEQ" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -59,6 +59,20 @@
FASTA output line width (default: 60)
.RE
.PP
+\fB\-contractdnawc\fR
+.RS 4
+replace stretches of DNA wildcards with a single
+\fIN\fR
+(default: no)
+.RE
+.PP
+\fB\-contractproteinwc\fR
+.RS 4
+replace stretches of protein wildcards with a single
+\fIX\fR
+(default: no)
+.RE
+.PP
\fB\-o\fR
.RS 4
redirect output to specified file (default: undefined)
Modified: trunk/packages/genometools/trunk/debian/man/gt-dupfeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-dupfeat.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-dupfeat.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-dupfeat
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-DUPFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-DUPFEAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Added: trunk/packages/genometools/trunk/debian/man/gt-encseq-bench.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-bench.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-bench.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: gt-encseq-bench
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 10/07/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-ENCSEQ\-BENCH" "1" "10/07/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * 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-bench \- Perform benchmark on extractions from encseq\&.
+.SH "SYNOPSIS"
+.sp
+gt encseq bench [option \&...] indexname
+.SH "OPTIONS"
+.PP
+\fB\-ccext\fR
+.RS 4
+specify number of random character extractions (default: 0)
+.RE
+.PP
+\fB\-solepr\fR
+.RS 4
+prepare data structure for sequences ordered by their length (default: no)
+.RE
+.PP
+\fB\-sain\fR
+.RS 4
+run induced suffix sorting in given mode (default: 0)
+.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>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq-bitextract.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-bitextract.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-bitextract.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq-bitextract
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ\-BITEXTRA" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ\-BITEXTRA" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq-check.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-check.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-check.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq-check
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ\-CHECK" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ\-CHECK" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -49,6 +49,16 @@
prefix length (default: 0)
.RE
.PP
+\fB\-nocheckunit\fR
+.RS 4
+do not run checkextractunitatpos (default: no)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
\fB\-help\fR
.RS 4
display help and exit
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq-decode.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-decode.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-decode.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq-decode
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ\-DECODE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ\-DECODE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq-encode.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-encode.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-encode.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq-encode
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ\-ENCODE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ\-ENCODE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq-info.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-info.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-info.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq-info
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ\-INFO" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ\-INFO" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq-md5.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq-md5.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq-md5.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq-md5
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ\-MD5" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ\-MD5" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -47,7 +47,7 @@
.sp
Tools:
.sp
-bitextract check decode encode info md5
+bench bitextract check decode encode info md5
.SH "AUTHOR"
.sp
Report bugs to <gt\-users at genometools\&.org>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-encseq2spm.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-encseq2spm.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-encseq2spm.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-encseq2spm
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ENCSEQ2SPM" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ENCSEQ2SPM" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-eval.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-eval.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-eval.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-eval
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-EVAL" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-EVAL" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -85,7 +85,7 @@
.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\&.
+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 numbe r 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>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-extractfeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-extractfeat.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-extractfeat.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-extractfeat
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-EXTRACTFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-EXTRACTFEAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-extractseq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-extractseq.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-extractseq.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-extractseq
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-EXTRACTSEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-EXTRACTSEQ" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -90,7 +90,7 @@
.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
+The option \-keys allows one 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
@@ -108,11 +108,11 @@
.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
+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 \&.\&.]
+gt suffixerator \-protein \-ssp \-tis \-des \-sds \-kys \-indexname fastaindex \-db inp utfile1 [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
@@ -126,7 +126,7 @@
.sp -1
.IP \(bu 2.3
.\}
-they all have to be of the same length, not longer than 128, and not shorter than 1
+they all have to be of the same length, not longer than 128, and not shorte r than 1
.RE
.sp
.RS 4
Modified: trunk/packages/genometools/trunk/debian/man/gt-featureindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-featureindex.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-featureindex.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-featureindex
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-FEATUREINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-FEATUREINDEX" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Added: trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -0,0 +1,111 @@
+'\" t
+.\" Title: gt-fingerprint
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 10/07/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-FINGERPRINT" "1" "10/07/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * 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-fingerprint \- Compute MD5 fingerprints for each sequence given in sequence_file(s)\&.
+.SH "SYNOPSIS"
+.sp
+gt fingerprint [option \&...] sequence_file [\&...]
+.SH "OPTIONS"
+.PP
+\fB\-check\fR
+.RS 4
+compare all fingerprints contained in the given checklist file with checksums in given sequence_files(s)\&. The comparison is successful, if all fingerprints given in checkfile can be found in the sequence_file(s) in the exact same quantity and vice versa\&. (default: undefined)
+.RE
+.PP
+\fB\-duplicates\fR
+.RS 4
+show duplicate fingerprints from given sequence_file(s)\&. (default: no)
+.RE
+.PP
+\fB\-extract\fR
+.RS 4
+extract the sequence(s) with the given fingerprint from sequence_file(s) and show them on stdout\&. (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
+If neither option \-check nor option \-duplicates is used, the fingerprints for all sequences are shown on stdout\&.
+.SH "EXAMPLES:"
+.sp
+Compute (unified) list of fingerprints:
+.sp
+$ gt fingerprint U89959_ests\&.fas | sort | uniq > U89959_ests\&.checklist_uniq
+.sp
+Compare fingerprints:
+.sp
+$ gt fingerprint \-check U89959_ests\&.checklist_uniq U89959_ests\&.fas 950b7715ab6cc030a8c810a0dba2dd33 only in sequence_file(s)
+.sp
+Make sure a sequence file contains no duplicates (not the case here):
+.sp
+$ gt fingerprint \-duplicates U89959_ests\&.fas 950b7715ab6cc030a8c810a0dba2dd33 2 gt fingerprint: error: duplicates found: 1 out of 200 (0\&.500%)
+.sp
+Extract sequence with given fingerprint:
+.sp
+$ gt fingerprint \-extract 6d3b4b9db4531cda588528f2c69c0a57 U89959_ests\&.fas >SQ;8720010 TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTTACATGATACCAACGTAATG GGAGCTTAAAAATA
+.SH "RETURN VALUES:"
+.sp
+0 everything went fine (\-check: the comparison was successful; \-duplicates: no duplicates found) 1 an error occured (\-check: the comparison was not successful; \-duplicates: duplicates found)
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-genomediff.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-genomediff.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-genomediff.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-genomediff
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-GENOMEDIFF" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-GENOMEDIFF" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -28,39 +28,56 @@
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
-gt-genomediff \- Calculates shulens of Genomes and the Kr\&.
+gt-genomediff \- Calculates Kr: pairwise distances between genomes\&.
.SH "SYNOPSIS"
.sp
-gt genomediff [option \&...] \-pck|\-esa indexname
+gt genomediff [option \&...] (INDEX | \-indexname NAME SEQFILE SEQFILE [\&...])
.SH "OPTIONS"
.PP
-\fB\-v\fR
+\fB\-indextype\fR
.RS 4
-be verbose (default: no)
+specify type of index, one of: esa|pck|encseq\&. Where encseq is an encoded sequence and an enhanced suffix array will be constructed only in memory\&. (default: encseq)
.RE
.PP
-\fB\-esa\fR
+\fB\-indexname\fR
.RS 4
-Specify index (enhanced suffix array) (default: undefined)
+Basename of encseq to construct\&. (default: undefined)
.RE
.PP
-\fB\-pck\fR
+\fB\-unitfile\fR
.RS 4
-Specify index (packed index) (default: undefined)
+specifies genomic units, see below for description\&. (default: undefined)
.RE
.PP
-\fB\-unitfile\fR
+\fB\-mirrored\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)
+virtually append the reverse complement of each sequence (default: no)
.RE
.PP
-\fB\-scan\fR
+\fB\-pl\fR
.RS 4
-do not load esa index but scan it sequentially (default: yes)
+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\-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\-help\fR
.RS 4
display help for basic options and exit
@@ -75,6 +92,32 @@
.RS 4
display version information and exit
.RE
+.SH "DESCRIPTION"
+.sp
+The genomediff tool only accepts DNA input\&.
+.sp
+When used with sequence files or encseq, an enhanced suffix array will be built in memory\&. The ESA will not be created completely, but construction will use \-memlimit as a threshold and build it partwise, calculating the Shu\-length for each part\&.
+.sp
+File format for option \-unitfile (lua):
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+units = {
+ genome1 = { "path/file1\&.fa", "file2\&.fa" },
+ genome2 = { "file3\&.fa", "path/file4\&.fa" }
+}
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+Give the path to the files as they were given to the encseq tool! You can use gt encseq info INDEXNAME to get a list of files in an encoded sequence\&.
+.sp
+Comment lines start with \fI\-\-\fR and will be ignored\&. See GTDIR/testdata/genomediff/unitfile1\&.lua for an example\&.
+.sp
+Options \-pl \-dc \-memlimit are options to influence esa construction\&.
.SH "AUTHOR"
.sp
Report bugs to <willrodt at zbh\&.uni\-hamburg\&.de>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-gff3.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gff3.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-gff3.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-gff3
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-GFF3" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-GFF3" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-gff3_to_gtf.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gff3_to_gtf.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-gff3_to_gtf.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" 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
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-GFF3_TO_GTF" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-GFF3_TO_GTF" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-gff3validator.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gff3validator.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-gff3validator.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-gff3validator
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-GFF3VALIDATOR" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-GFF3VALIDATOR" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-gtf_to_gff3.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-gtf_to_gff3.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-gtf_to_gff3.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" 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
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-GTF_TO_GFF3" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-GTF_TO_GFF3" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Added: trunk/packages/genometools/trunk/debian/man/gt-hop.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-hop.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-hop.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -0,0 +1,139 @@
+'\" t
+.\" Title: gt-hop
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 10/07/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-HOP" "1" "10/07/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * 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-hop \- Reference\-based homopolymer error correction\&.
+.SH "SYNOPSIS"
+.sp
+gt hop \-<mode> \-ref <encseq> \-map <sam/bam> \-reads <fastq> [options\&...]
+.SH "OPTIONS"
+.PP
+\fB\-ref\fR
+.RS 4
+reference sequence in GtEncseq format (can be prepared using gt encseq encode)
+.RE
+.PP
+\fB\-map\fR
+.RS 4
+mapping of reads to reference it must be in SAM/BAM format, and sorted by coordinate (can be prepared e\&.g\&. using: samtools sort)
+.RE
+.PP
+\fB\-sam\fR
+.RS 4
+mapping file is SAM (default: BAM)
+.RE
+.PP
+\fB\-aggressive\fR
+.RS 4
+correct as much as possible
+.RE
+.PP
+\fB\-moderate\fR
+.RS 4
+mediate between sensitivity and precision
+.RE
+.PP
+\fB\-conservative\fR
+.RS 4
+correct only most likely errors
+.RE
+.PP
+\fB\-expert\fR
+.RS 4
+manually select correction criteria
+.RE
+.PP
+\fB\-reads\fR
+.RS 4
+uncorrected read file(s) in FastQ format; the corrected reads are output in the currect working directory in files which are named as the input files, each prepended by a prefix (see \-outprefix option) \-reads allows to output the reads in the same order as in the input and is mandatory if the SAM contains more than a single primary alignment for each read (e\&.g\&. output of bwasw) see also \-o option as an alternative
+.RE
+.PP
+\fB\-outprefix\fR
+.RS 4
+prefix for output filenames (corrected reads)when \-reads is specified the prefix is prepended to each input filename (default: hop_)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+output file for corrected reads (see also \-reads/\-outprefix) if \-o is used, reads are output in a single file in the order they are found in the SAM file (which usually differ from the original order) this will only work if the reads were aligned with a software which only includes 1 alignment for each read (e\&.g\&. bwa) (default: undefined)
+.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 "DESCRIPTION"
+.sp
+Correction mode:
+.sp
+One of the options \-aggressive, \-moderate, \-conservative or \-expert must be selected\&.
+.sp
+The \-aggressive, \-moderate and \-conservative modes are presets of the criteria by which it is decided if an observed discrepancy in homopolymer length between reference and a read shall be corrected or not\&. A description of the single criteria is provided by using the \-help+ option\&. The presets are equivalent to the following settings:
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+ \-aggressive \-moderate \-conservative
+\-hmin 3 3 3
+\-read\-hmin 1 1 2
+\-altmax 1\&.00 0\&.99 0\&.80
+\-refmin 0\&.00 0\&.00 0\&.10
+\-mapqmin 0 10 21
+\-covmin 1 1 1
+\-clenmax unlimited unlimited unlimited
+\-allow\-multiple yes yes no
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+The aggressive mode tries to maximize the sensitivity, the conservative mode to minimize the false positives\&. An even more conservative set of corrections can be achieved using the \-ann option (see \-help+)\&.
+.sp
+The \-expert mode allows to manually set each parameter; the default values are the same as in the \-conservative mode\&.
+.sp
+(Finally, for evaluation purposes only, the \-state\-of\-truth mode can be used: this mode assumes that the target sequence of the sequencing has been specified as reference sequence and outputs an ideal list of corrections\&.)
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-id_to_md5.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-id_to_md5.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-id_to_md5.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" 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
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ID_TO_MD5" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ID_TO_MD5" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-interfeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-interfeat.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-interfeat.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-interfeat
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-INTERFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-INTERFEAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-ltrclustering.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-ltrclustering.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-ltrclustering.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-ltrclustering
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-LTRCLUSTERING" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-LTRCLUSTERING" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-ltrdigest.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-ltrdigest.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-ltrdigest.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-ltrdigest
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-LTRDIGEST" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-LTRDIGEST" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -59,6 +59,11 @@
required U\-box length range (default: 3 30)
.RE
.PP
+\fB\-uboxdist\fR
+.RS 4
+allowed U\-box distance range from PPT (default: 0)
+.RE
+.PP
\fB\-pptradius\fR
.RS 4
radius around beginning of 3\*(Aq LTR to search for PPT (default: 30)
Modified: trunk/packages/genometools/trunk/debian/man/gt-ltrharvest.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-ltrharvest.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-ltrharvest.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-ltrharvest
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-LTRHARVEST" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-LTRHARVEST" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-matchtool.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-matchtool.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-matchtool.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-matchtool
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MATCHTOOL" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MATCHTOOL" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-matstat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-matstat.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-matstat.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-matstat
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MATSTAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MATSTAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-md5_to_id.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-md5_to_id.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-md5_to_id.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" 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
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MD5_TO_ID" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MD5_TO_ID" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-merge.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-merge.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-merge.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-merge
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MERGE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MERGE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-mergefeat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mergefeat.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-mergefeat.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-mergefeat
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MERGEFEAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MERGEFEAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-mgth.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mgth.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-mgth.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-mgth
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MGTH" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MGTH" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-mkfeatureindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mkfeatureindex.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-mkfeatureindex.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-mkfeatureindex
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MKFEATUREINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MKFEATUREINDEX" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-mkfmindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mkfmindex.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-mkfmindex.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-mkfmindex
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MKFMINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MKFMINDEX" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-mmapandread.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-mmapandread.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-mmapandread.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-mmapandread
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-MMAPANDREAD" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-MMAPANDREAD" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-orffinder.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-orffinder.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-orffinder.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-orffinder
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-ORFFINDER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-ORFFINDER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-packedindex-chkintegrity.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-chkintegrity.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-chkintegrity.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-packedindex-chkintegrity
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-PACKEDINDEX\-CHK" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-PACKEDINDEX\-CHK" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-packedindex-chksearch.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-chksearch.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-chksearch.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-packedindex-chksearch
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-PACKEDINDEX\-CHK" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-PACKEDINDEX\-CHK" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkctxmap.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkctxmap.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkctxmap.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-packedindex-mkctxmap
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-PACKEDINDEX\-MKC" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-PACKEDINDEX\-MKC" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkindex.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-mkindex.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-packedindex-mkindex
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-PACKEDINDEX\-MKI" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-PACKEDINDEX\-MKI" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -96,7 +96,7 @@
.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)
+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
@@ -109,6 +109,11 @@
output/sort according to keys of the form |key| in fasta header (default: nosort)
.RE
.PP
+\fB\-dir\fR
+.RS 4
+specify reading direction (fwd, cpl, rev, rcl) (default: fwd)
+.RE
+.PP
\fB\-bsize\fR
.RS 4
specify size of blocks (default: 8)
@@ -144,11 +149,6 @@
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)
Modified: trunk/packages/genometools/trunk/debian/man/gt-packedindex-trsuftab.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex-trsuftab.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex-trsuftab.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-packedindex-trsuftab
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-PACKEDINDEX\-TRS" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-PACKEDINDEX\-TRS" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-packedindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-packedindex.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-packedindex.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-packedindex
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-PACKEDINDEX" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-PACKEDINDEX" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-prebwt.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-prebwt.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-prebwt.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-prebwt
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-PREBWT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-PREBWT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-readjoiner-assembly.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner-assembly.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner-assembly.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-readjoiner-assembly
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-READJOINER\-ASSE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-READJOINER\-ASSE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-readjoiner-overlap.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner-overlap.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner-overlap.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-readjoiner-overlap
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-READJOINER\-OVER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-READJOINER\-OVER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-readjoiner-prefilter.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner-prefilter.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner-prefilter.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-readjoiner-prefilter
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-READJOINER\-PREF" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-READJOINER\-PREF" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -28,7 +28,7 @@
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
-gt-readjoiner-prefilter \- Remove contained reads and reads containing ambiguity codes in given sequence_file(s)\&.
+gt-readjoiner-prefilter \- Remove contained and low\-quality reads and encode read set in GtEncseq format\&.
.SH "SYNOPSIS"
.sp
gt readjoiner prefilter [option \&...]
@@ -41,7 +41,9 @@
.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
+specify a list of input libraries (Fasta/FastQ); for single\-end libraries use the filename (which is not allowed to contain
+\fI:\fR
+symbols); for paired\-end libraries with reads interleaved (f,r,f,r,\&...) in a single file use the notation <filename>:<insertlength>[,<stdev>] (stdev may be omitted); for paired\-end with reads in two files (f, r) use the notation <file_f>:<file_r>:<insertlength>[,<stdev>]
.RE
.PP
\fB\-v\fR
@@ -56,9 +58,14 @@
.PP
\fB\-help\fR
.RS 4
-display help and exit
+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
Modified: trunk/packages/genometools/trunk/debian/man/gt-readjoiner.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-readjoiner.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-readjoiner.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-readjoiner
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-READJOINER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-READJOINER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-repfind.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-repfind.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-repfind.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-repfind
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-REPFIND" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-REPFIND" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-scriptfilter.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-scriptfilter.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-scriptfilter.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-scriptfilter
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SCRIPTFILTER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SCRIPTFILTER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-select.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-select.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-select.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-select
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SELECT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SELECT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-seq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seq.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seq.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seq
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQ" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQ" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-seqfilter.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqfilter.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqfilter.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seqfilter
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQFILTER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQFILTER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-seqids.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqids.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqids.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seqids
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQIDS" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQIDS" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-seqmutate.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqmutate.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqmutate.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seqmutate
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQMUTATE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQMUTATE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -75,7 +75,7 @@
.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
+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 i s 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"
Modified: trunk/packages/genometools/trunk/debian/man/gt-seqorder.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqorder.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqorder.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seqorder
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQORDER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQORDER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-seqstat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqstat.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqstat.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seqstat
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQSTAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQSTAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-seqtransform.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqtransform.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqtransform.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seqtransform
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQTRANSFORM" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQTRANSFORM" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-seqtranslate.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-seqtranslate.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-seqtranslate.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-seqtranslate
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQTRANSLATE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQTRANSLATE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-sequniq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-sequniq.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-sequniq.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-sequniq
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SEQUNIQ" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SEQUNIQ" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-shredder.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-shredder.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-shredder.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-shredder
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SHREDDER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SHREDDER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-shulengthdist.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-shulengthdist.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-shulengthdist.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-shulengthdist
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SHULENGTHDIST" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SHULENGTHDIST" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-simreads.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-simreads.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-simreads.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-simreads
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SIMREADS" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SIMREADS" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-sketch.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-sketch.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-sketch.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-sketch
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SKETCH" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SKETCH" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-sketch_page.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-sketch_page.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-sketch_page.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-sketch_page
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SKETCH_PAGE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SKETCH_PAGE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-splicesiteinfo.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-splicesiteinfo.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-splicesiteinfo.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-splicesiteinfo
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SPLICESITEINFO" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SPLICESITEINFO" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-splitfasta.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-splitfasta.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-splitfasta.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-splitfasta
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SPLITFASTA" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SPLITFASTA" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-stat.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-stat.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-stat.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-stat
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-STAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-STAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-suffixerator.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-suffixerator.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-suffixerator.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-suffixerator
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-SUFFIXERATOR" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-SUFFIXERATOR" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -96,7 +96,7 @@
.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)
+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
@@ -104,11 +104,30 @@
specify difference cover value (default: 0)
.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\-kys\fR
.RS 4
output/sort according to keys of the form |key| in fasta header (default: nosort)
.RE
.PP
+\fB\-dir\fR
+.RS 4
+specify reading direction (fwd, cpl, rev, rcl) (default: fwd)
+.RE
+.PP
\fB\-suf\fR
.RS 4
output suffix array (suftab) to file (default: no)
@@ -129,25 +148,6 @@
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)
Modified: trunk/packages/genometools/trunk/debian/man/gt-tagerator.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tagerator.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-tagerator.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-tagerator
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-TAGERATOR" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-TAGERATOR" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-tallymer-mkindex.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer-mkindex.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer-mkindex.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-tallymer-mkindex
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-TALLYMER\-MKINDE" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-TALLYMER\-MKINDE" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-tallymer-occratio.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer-occratio.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer-occratio.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-tallymer-occratio
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-TALLYMER\-OCCRAT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-TALLYMER\-OCCRAT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-tallymer-search.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer-search.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer-search.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-tallymer-search
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-TALLYMER\-SEARCH" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-TALLYMER\-SEARCH" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-tallymer.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-tallymer.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-tallymer.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-tallymer
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-TALLYMER" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-TALLYMER" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt-uniq.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-uniq.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-uniq.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-uniq
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-UNIQ" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-UNIQ" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -72,11 +72,11 @@
.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\&.
+Two feature node graphs are considered to be repeated if their feature node lis t (from the depth\-first traversal) have the same length and each feature node pai r (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\&.
+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 define d score, this one is kept\&.
.SH "AUTHOR"
.sp
Report bugs to <gt\-users at genometools\&.org>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-uniquesub.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-uniquesub.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt-uniquesub.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt-uniquesub
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-UNIQUESUB" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT\-UNIQUESUB" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
Modified: trunk/packages/genometools/trunk/debian/man/gt.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt.1 2012-10-07 13:47:03 UTC (rev 12323)
+++ trunk/packages/genometools/trunk/debian/man/gt.1 2012-10-07 17:33:05 UTC (rev 12324)
@@ -2,12 +2,12 @@
.\" Title: gt
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 07/11/2012
+.\" Date: 10/07/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT" "1" "07/11/2012" "\ \&" "\ \&"
+.TH "GT" "1" "10/07/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -60,11 +60,11 @@
.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
+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 hop 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\&.
+Set the environment variable GT_ENV_OPTIONS=\-spacepeak to show a spacepeak afte r 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"
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