[med-svn] [SCM] cufflinks branch, master, updated. upstream/0.9.3-21-g7df8ccc
Alex Mestiashvili
alex at biotec.tu-dresden.de
Wed May 25 07:53:09 UTC 2011
The following commit has been merged in the master branch:
commit 528140cf82e42b2a7b7ff3e5532bea1529072e36
Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
Date: Tue May 24 13:43:09 2011 +0200
Imported Debian patch 1.0.2-1
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5b3ecc2
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,11 @@
+cufflinks (1.0.2-1) unstable; urgency=low
+
+ * Upstream release
+
+ -- Alex Mestiashvili <alex at biotec.tu-dresden.de> Tue, 24 May 2011 13:43:09 +0200
+
+cufflinks (0.9.3-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Alex Mestiashvili <alex at biotec.tu-dresden.de> Tue, 03 May 2011 13:53:19 +0000
diff --git a/debian/compat b/debian/compat
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index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/compress_gtf.1 b/debian/compress_gtf.1
new file mode 100644
index 0000000..c7a7877
--- /dev/null
+++ b/debian/compress_gtf.1
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4.
+.TH COMPRESS_GTF: "1" "May 2011" "compress_gtf" "User Commands"
+.SH NAME
+compress_gtf: \- compress_gtf
+.SH SYNOPSIS
+.B compress_gtf
+[\fIoptions\fR] \fI<reference.gtf> <compressed_reference.gtf>\fR
+.SH OPTIONS
+\fB\-r\fR/\-\-reference\-seq reference fasta file [ default: NULL ]
+
+\fB\-F\fR/\-\-raw\-fpkm use FPKM instead of isoform fraction
+
+\fB\-U\fR/\-\-union report projective union [ default: OFF ]
+
+\fB\-I\fR/\-\-intersection report projective intersection [ default: ON ]
+
+.PP
+.SH SEE ALSO
+http://cufflinks.cbcb.umd.edu/manual.html
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..6687089
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,21 @@
+Source: cufflinks
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Build-Depends: debhelper (>= 7.0.50~), autotools-dev , libboost-dev (>=1.38.0) , libbam-dev
+Standards-Version: 3.9.2
+Homepage: http://cufflinks.cbcb.umd.edu/
+Vcs-Git: git://git.debian.org/debian-med/cufflinks.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary
+
+Package: cufflinks
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Description: Transcript assembly, differential expression and regulation for RNA-Seq
+ Cufflinks assembles transcripts, estimates their abundances, and tests for
+ differential expression and regulation in RNA-Seq samples. It accepts aligned
+ RNA-Seq reads and assembles the alignments into a parsimonious set of
+ transcripts. Cufflinks then estimates the relative abundances of these
+ transcripts based on how many reads support each one.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..c5c508b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,40 @@
+Format : http://dep.debian.net/deps/dep5
+Upstream-Name : cufflinks
+Source : http://cufflinks.cbcb.umd.edu/downloads/
+
+Files: *
+Copyright: Copyright (C) 2003-2009 Cole Trapnell et al
+License: BSL-1
+
+Files: debian/*
+Copyright: 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+License: BSL-1
+
+License : BSL-1
+
+ ===========================================================================
+ Boost Software License, Version 1.0
+ ===========================================================================
+
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
diff --git a/debian/cuffcompare.1 b/debian/cuffcompare.1
new file mode 100644
index 0000000..5138968
--- /dev/null
+++ b/debian/cuffcompare.1
@@ -0,0 +1,53 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4.
+.TH CUFFCOMPARE "1" "May 2011" "cuffcompare v1.0.2 (2335)" "User Commands"
+.SH NAME
+cuffcompare \- helps analyze the transfrags
+.SH SYNOPSIS
+cuffcompare [\-r <reference_mrna.gtf>] [\-R] [\-T] [\-V] [\-s <seq_path>]
+.IP
+[\-o <outprefix>] [\-p <cprefix>]
+{\-i <input_gtf_list> | <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}
+
+.IP
+.SH DESCRIPTION
+Cuffcompare provides classification, reference annotation mapping and various
+statistics for Cufflinks transfrags.
+Cuffcompare clusters and tracks transfrags across multiple samples, writing
+matching transcripts (intron chains) into <outprefix>.tracking, and a GTF
+file <outprefix>.combined.gtf containing a nonredundant set of transcripts
+across all input files (with a single representative transfrag chosen
+for each clique of matching transfrags across samples).
+.SH OPTIONS
+\fB\-i\fR provide a text file with a list of Cufflinks GTF files to process instead
+.IP
+of expecting them as command line arguments (useful when a large number
+of GTF files should be processed)
+.PP
+\fB\-r\fR a set of known mRNAs to use as a reference for assessing
+.IP
+the accuracy of mRNAs or gene models given in <input.gtf>
+.PP
+\fB\-R\fR for \fB\-r\fR option, reduce the set of reference transcripts to
+.IP
+only those found to overlap any of the input loci
+.PP
+\fB\-M\fR discard (ignore) single\-exon transfrags and reference transcripts
+\fB\-N\fR discard (ignore) single\-exon reference transcripts
+.PP
+\fB\-s\fR <seq_path> can be a multi\-fasta file with all the genomic sequences or
+.IP
+a directory containing multiple single\-fasta files (one file per contig);
+lower case bases will be used to classify input transcripts as repeats
+.PP
+\fB\-d\fR max distance (range) for grouping transcript start sites (100)
+\fB\-p\fR the name prefix to use for consensus transcripts in the
+.IP
+<outprefix>.combined.gtf file (default: 'TCONS')
+.PP
+\fB\-C\fR include the "contained" transcripts in the .combined.gtf file
+\fB\-G\fR generic GFF input file(s) (do not assume Cufflinks GTF)
+\fB\-T\fR do not generate .tmap and .refmap files for each input file
+\fB\-V\fR verbose processing mode (showing all GFF parsing warnings)
+.PP
+.SH SEE ALSO
+http://cufflinks.cbcb.umd.edu/manual.html#cuffcompare
diff --git a/debian/cuffdiff.1 b/debian/cuffdiff.1
new file mode 100644
index 0000000..734eae6
--- /dev/null
+++ b/debian/cuffdiff.1
@@ -0,0 +1,90 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4.
+.TH CUFFDIFF: "1" "May 2011" "cuffdiff" "User Commands"
+.SH NAME
+cuffdiff \- find significant changes in transcript expression, splicing, and promoter use
+.SH SYNOPSIS
+.B cuffdiff
+[\fIoptions\fR] \fI<transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> \fR[... \fIsampleN_hits.sam\fR]
+
+Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam
+.SH DESCRIPTION
+see online page http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
+.SH OPTIONS
+.TP
+\fB\-o\fR/\-\-output\-dir
+write all output files to this directory [ default: ./ ]
+.TP
+\fB\-T\fR/\-\-time\-series
+treat samples as a time\-series [ default: FALSE ]
+.TP
+\fB\-c\fR/\-\-min\-alignment\-count
+minimum number of alignments in a locus for testing [ default: 10 ]
+.TP
+\fB\-\-FDR\fR
+False discovery rate used in testing [ default: 0.05 ]
+.TP
+\fB\-M\fR/\-\-mask\-file
+ignore all alignment within transcripts in this file [ default: NULL ]
+.TP
+\fB\-b\fR/\-\-frag\-bias\-correct
+use bias correction \- reference fasta required [ default: NULL ]
+.TP
+\fB\-u\fR/\-\-multi\-read\-correct
+use 'rescue method' for multi\-reads (more accurate) [ default: FALSE ]
+.TP
+\fB\-N\fR/\-\-upper\-quartile\-norm
+use upper\-quartile normalization [ default: FALSE ]
+.TP
+\fB\-L\fR/\-\-labels
+comma\-separated list of condition labels
+.TP
+\fB\-p\fR/\-\-num\-threads
+number of threads used during quantification [ default: 1 ]
+.SS "Advanced Options:"
+.TP
+\fB\-\-library\-type\fR
+Library prep used for input reads [ default: below ]
+.TP
+\fB\-m\fR/\-\-frag\-len\-mean
+average fragment length (unpaired reads only) [ default: 200 ]
+.TP
+\fB\-s\fR/\-\-frag\-len\-std\-dev
+fragment length std deviation (unpaired reads only) [ default: 80 ]
+.TP
+\fB\-\-num\-importance\-samples\fR
+number of importance samples for MAP restimation [ default: 1000 ]
+.TP
+\fB\-\-max\-mle\-iterations\fR
+maximum iterations allowed for MLE calculation [ default: 5000 ]
+.TP
+\fB\-\-compatible\-hits\-norm\fR
+count hits compatible with reference RNAs only [ default: TRUE ]
+.TP
+\fB\-\-total\-hits\-norm\fR
+count all hits for normalization [ default: FALSE ]
+.TP
+\fB\-\-poisson\-dispersion\fR
+Don't fit fragment counts for overdispersion [ default: FALSE ]
+.TP
+\fB\-v\fR/\-\-verbose
+log\-friendly verbose processing (no progress bar) [ default: FALSE ]
+.TP
+\fB\-q\fR/\-\-quiet
+log\-friendly quiet processing (no progress bar) [ default: FALSE ]
+.TP
+\fB\-\-no\-update\-check\fR
+do not contact server to check for update availability[ default: FALSE ]
+.TP
+\fB\-\-emit\-count\-tables\fR
+print count tables used to fit overdispersion [ default: FALSE ]
+.SS "Supported library types:"
+.IP
+ff\-firststrand
+ff\-secondstrand
+ff\-unstranded
+fr\-firststrand
+fr\-secondstrand
+fr\-unstranded (default)
+transfrags
+.PP
+
diff --git a/debian/cufflinks.1 b/debian/cufflinks.1
new file mode 100644
index 0000000..3dfe393
--- /dev/null
+++ b/debian/cufflinks.1
@@ -0,0 +1,240 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4.
+.TH CUFFLINKS: "1" "May 2011" "cufflinks v1.0.2 '" "User Commands"
+.SH NAME
+cufflinks \- Transcript assembly, differential expression, and differential regulation for RNA-Seq
+.SH DESCRIPTION
+see online page http://cufflinks.cbcb.umd.edu/manual.html
+.SH SYNOPSIS
+.B cufflinks
+[\fIoptions\fR] \fI<hits.sam>\fR
+.SH OPTIONS
+.TP
+\fB\-o\fR/\-\-output\-dir
+write all output files to this directory [ default: ./ ]
+.TP
+\fB\-p\fR/\-\-num\-threads
+number of threads used during analysis [ default: 1 ]
+.TP
+\fB\-G\fR/\-\-GTF
+quantitate against reference transcript annotations
+.TP
+\fB\-g\fR/\-\-GTF\-guide
+use reference transcript annotation to guide assembly
+.TP
+\fB\-M\fR/\-\-mask\-file
+ignore all alignment within transcripts in this file
+.TP
+\fB\-b\fR/\-\-frag\-bias\-correct
+use bias correction \- reference fasta required [ default: NULL ]
+.TP
+\fB\-u\fR/\-\-multi\-read\-correct
+use 'rescue method' for multi\-reads (more accurate) [ default: FALSE ]
+.TP
+\fB\-\-library\-type\fR
+library prep used for input reads [ default: below ]
+.SS "Advanced Abundance Estimation Options:"
+.TP
+\fB\-m\fR/\-\-frag\-len\-mean
+average fragment length (unpaired reads only) [ default: 200 ]
+.TP
+\fB\-s\fR/\-\-frag\-len\-std\-dev
+fragment length std deviation (unpaired reads only) [ default: 80 ]
+.TP
+\fB\-\-upper\-quartile\-norm\fR
+use upper\-quartile normalization [ default: FALSE ]
+.TP
+\fB\-\-max\-mle\-iterations\fR
+maximum iterations allowed for MLE calculation [ default: 5000 ]
+.TP
+\fB\-\-num\-importance\-samples\fR
+number of importance samples for MAP restimation [ default: 1000 ]
+.TP
+\fB\-\-compatible\-hits\-norm\fR
+count hits compatible with reference RNAs only [ default: FALSE ]
+.TP
+\fB\-\-total\-hits\-norm\fR
+count all hits for normalization [ default: TRUE ]
+.SS "Advanced Assembly Options:"
+.TP
+\fB\-L\fR/\-\-label
+assembled transcripts have this ID prefix [ default: CUFF ]
+.TP
+\fB\-F\fR/\-\-min\-isoform\-fraction
+suppress transcripts below this abundance level [ default: 0.10 ]
+.TP
+\fB\-j\fR/\-\-pre\-mrna\-fraction
+suppress intra\-intronic transcripts below this level [ default: 0.15 ]
+.TP
+\fB\-I\fR/\-\-max\-intron\-length
+ignore alignments with gaps longer than this [ default: 300000 ]
+.TP
+\fB\-a\fR/\-\-junc\-alpha
+alpha for junction binomial test filter [ default: 0.001 ]
+.TP
+\fB\-A\fR/\-\-small\-anchor\-fraction
+percent read overhang taken as 'suspiciously small' [ default: 0.09 ]
+.TP
+\fB\-\-min\-frags\-per\-transfrag\fR
+minimum number of fragments needed for new transfrags [ default: 10 ]
+.TP
+\fB\-\-overhang\-tolerance\fR
+number of terminal exon bp to tolerate in introns [ default: 8 ]
+.TP
+\fB\-\-max\-bundle\-length\fR
+maximum genomic length allowed for a given bundle [ default:3500000 ]
+.TP
+\fB\-\-min\-intron\-length\fR
+minimum intron size allowed in genome [ default: 50 ]
+.TP
+\fB\-\-trim\-3\-avgcov\-thresh\fR
+minimum avg coverage required to attempt 3' trimming [ default: 10 ]
+.TP
+\fB\-\-trim\-3\-dropoff\-frac\fR
+fraction of avg coverage below which to trim 3' end [ default: 0.1 ]
+.SS "Advanced Reference Annotation Guided Assembly Options:"
+.TP
+\fB\-\-no\-faux\-reads\fR
+disable tiling by faux reads [ default: FALSE ]
+.TP
+\fB\-\-3\-overhang\-tolerance\fR
+overhang allowed on 3' end when merging with reference[ default: 600 ]
+.TP
+\fB\-\-intron\-overhang\-tolerance\fR
+overhang allowed inside reference intron when merging [ default: 30 ]
+.SS "Advanced Program Behavior Options:"
+.TP
+\fB\-v\fR/\-\-verbose
+log\-friendly verbose processing (no progress bar) [ default: FALSE ]
+.TP
+\fB\-q\fR/\-\-quiet
+log\-friendly quiet processing (no progress bar) [ default: FALSE ]
+.TP
+\fB\-\-no\-update\-check\fR
+do not contact server to check for update availability[ default: FALSE ]
+.SS "Supported library types:"
+.IP
+ff\-firststrand
+ff\-secondstrand
+ff\-unstranded
+fr\-firststrand
+fr\-secondstrand
+fr\-unstranded (default)
+transfrags
+.PP
+cufflinks v1.0.2
+linked against Boost version 104601
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+Usage: cufflinks [options] <hits.sam>
+General Options:
+.TP
+\fB\-o\fR/\-\-output\-dir
+write all output files to this directory [ default: ./ ]
+.TP
+\fB\-p\fR/\-\-num\-threads
+number of threads used during analysis [ default: 1 ]
+.TP
+\fB\-G\fR/\-\-GTF
+quantitate against reference transcript annotations
+.TP
+\fB\-g\fR/\-\-GTF\-guide
+use reference transcript annotation to guide assembly
+.TP
+\fB\-M\fR/\-\-mask\-file
+ignore all alignment within transcripts in this file
+.TP
+\fB\-b\fR/\-\-frag\-bias\-correct
+use bias correction \- reference fasta required [ default: NULL ]
+.TP
+\fB\-u\fR/\-\-multi\-read\-correct
+use 'rescue method' for multi\-reads (more accurate) [ default: FALSE ]
+.TP
+\fB\-\-library\-type\fR
+library prep used for input reads [ default: below ]
+.SS "Advanced Abundance Estimation Options:"
+.TP
+\fB\-m\fR/\-\-frag\-len\-mean
+average fragment length (unpaired reads only) [ default: 200 ]
+.TP
+\fB\-s\fR/\-\-frag\-len\-std\-dev
+fragment length std deviation (unpaired reads only) [ default: 80 ]
+.TP
+\fB\-\-upper\-quartile\-norm\fR
+use upper\-quartile normalization [ default: FALSE ]
+.TP
+\fB\-\-max\-mle\-iterations\fR
+maximum iterations allowed for MLE calculation [ default: 5000 ]
+.TP
+\fB\-\-num\-importance\-samples\fR
+number of importance samples for MAP restimation [ default: 1000 ]
+.TP
+\fB\-\-compatible\-hits\-norm\fR
+count hits compatible with reference RNAs only [ default: FALSE ]
+.TP
+\fB\-\-total\-hits\-norm\fR
+count all hits for normalization [ default: TRUE ]
+.SS "Advanced Assembly Options:"
+.TP
+\fB\-L\fR/\-\-label
+assembled transcripts have this ID prefix [ default: CUFF ]
+.TP
+\fB\-F\fR/\-\-min\-isoform\-fraction
+suppress transcripts below this abundance level [ default: 0.10 ]
+.TP
+\fB\-j\fR/\-\-pre\-mrna\-fraction
+suppress intra\-intronic transcripts below this level [ default: 0.15 ]
+.TP
+\fB\-I\fR/\-\-max\-intron\-length
+ignore alignments with gaps longer than this [ default: 300000 ]
+.TP
+\fB\-a\fR/\-\-junc\-alpha
+alpha for junction binomial test filter [ default: 0.001 ]
+.TP
+\fB\-A\fR/\-\-small\-anchor\-fraction
+percent read overhang taken as 'suspiciously small' [ default: 0.09 ]
+.TP
+\fB\-\-min\-frags\-per\-transfrag\fR
+minimum number of fragments needed for new transfrags [ default: 10 ]
+.TP
+\fB\-\-overhang\-tolerance\fR
+number of terminal exon bp to tolerate in introns [ default: 8 ]
+.TP
+\fB\-\-max\-bundle\-length\fR
+maximum genomic length allowed for a given bundle [ default:3500000 ]
+.TP
+\fB\-\-min\-intron\-length\fR
+minimum intron size allowed in genome [ default: 50 ]
+.TP
+\fB\-\-trim\-3\-avgcov\-thresh\fR
+minimum avg coverage required to attempt 3' trimming [ default: 10 ]
+.TP
+\fB\-\-trim\-3\-dropoff\-frac\fR
+fraction of avg coverage below which to trim 3' end [ default: 0.1 ]
+.SS "Advanced Reference Annotation Guided Assembly Options:"
+.TP
+\fB\-\-no\-faux\-reads\fR
+disable tiling by faux reads [ default: FALSE ]
+.TP
+\fB\-\-3\-overhang\-tolerance\fR
+overhang allowed on 3' end when merging with reference[ default: 600 ]
+.TP
+\fB\-\-intron\-overhang\-tolerance\fR
+overhang allowed inside reference intron when merging [ default: 30 ]
+.SS "Advanced Program Behavior Options:"
+.TP
+\fB\-v\fR/\-\-verbose
+log\-friendly verbose processing (no progress bar) [ default: FALSE ]
+.TP
+\fB\-q\fR/\-\-quiet
+log\-friendly quiet processing (no progress bar) [ default: FALSE ]
+.TP
+\fB\-\-no\-update\-check\fR
+do not contact server to check for update availability[ default: FALSE ]
+.SS "Supported library types:"
+.IP
+ff\-firststrand
+ff\-secondstrand
+ff\-unstranded
+fr\-firststrand
+fr\-secondstrand
+fr\-unstranded (default)
+transfrags
diff --git a/debian/cufflinks.manpages b/debian/cufflinks.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/cufflinks.manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/cuffmerge.1 b/debian/cuffmerge.1
new file mode 100644
index 0000000..c62b971
--- /dev/null
+++ b/debian/cuffmerge.1
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4.
+.TH CUFFMERGE "1" "May 2011" "merge_cuff_asms v1.0.0" "User Commands"
+.SH NAME
+cuffmerge \- Merging assemblies
+.SH DESCRIPTION
+cuffmerge takes two or more Cufflinks GTF files and merges them into a
+single unified transcript catalog. Optionally, you can provide the script
+with a reference GTF, and the script will use it to attach gene names and other
+metadata to the merged catalog.
+.SH SYNOPSIS
+cuffmerge [Options] <assembly_GTF_list.txt>
+.SH OPTIONS
+.TP
+\fB\-h\fR/\-\-help
+Prints the help message and exits
+.TP
+\fB\-o\fR
+<output_dir> Directory where merged assembly will be written [ default: ./merged_asm ]
+.TP
+\fB\-g\fR/\-\-ref\-gtf
+An optional "reference" annotation GTF.
+.TP
+\fB\-s\fR/\-\-ref\-sequence
+<seq_dir>/<seq_fasta> Genomic DNA sequences for the reference.
+.TP
+\fB\-\-min\-isoform\-fraction\fR <0\-1.0>
+Discard isoforms with abundance below this [ default: 0.5 ]
+.TP
+\fB\-p\fR/\-\-num\-threads
+<int> Use this many threads to merge assemblies. [ default: 1 ]
+.TP
+\fB\-\-keep\-tmp\fR
+Keep all intermediate files during merge
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README
diff --git a/debian/gffread.1 b/debian/gffread.1
new file mode 100644
index 0000000..5499117
--- /dev/null
+++ b/debian/gffread.1
@@ -0,0 +1,219 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4.
+.TH GFFREAD "1" "May 2011" "gffread Usage:" "User Commands"
+.SH NAME
+gffread \- one of the cufflinks tools
+.SH SYSNOPSIS
+gffread <input_gff> [\-g <genomic_seqs_fasta> | <dir>][\-s <seq_info.fsize>]
+.IP
+[\-o <outfile.gff>] [\-t <tname>] [\-r [[<strand>]<chr>:]<start>..<end>]
+[\-CTVNMAFGRUVBHSZWTOE] [\-w <spl_exons.fa>] [\-x <spl_cds.fa>] [\-y <tr_cds.fa>]
+[\-i <maxintron>]
+Filters and/or converts GFF3/GTF2 records.
+<input_gff> is a GFF file, use '\-' if the GFF records will be given at stdin
+.IP
+.SH Options
+.TP
+\fB\-g\fR
+full path to a multi\-fasta file with the genomic sequences
+for all input mappings, OR a directory with single\-fasta files
+(one per genomic sequence, with file names matching sequence names)
+.TP
+\fB\-s\fR
+<seq_info.fsize> is a tab\-delimited file providing this info
+for each of the mapped sequences:
+<seq\-name> <seq\-length> <seq\-description>
+(useful for mRNA/EST/protein mappings with \fB\-A\fR option)
+.TP
+\fB\-i\fR
+discard transcripts having an intron larger than <maxintron>
+.TP
+\fB\-r\fR
+only show transcripts crossing coordinate range <start>..<end>
+(on chromosome/contig <chr>, strand <strand> if provided)
+.TP
+\fB\-R\fR
+for \fB\-r\fR option, discard all transcripts that are not fully
+contained within given range
+.TP
+\fB\-U\fR
+discard single\-exon transcripts
+.TP
+\fB\-C\fR
+discard mRNAs that have no CDS feature
+.TP
+\fB\-F\fR
+keep all attributes from last column of GFF/GTF
+.TP
+\fB\-G\fR
+only parse additional exon attributes from the first exon
+and move them to the mRNA level (useful for GTF input)
+.TP
+\fB\-A\fR
+use the description field from <seq_info.fsize> and add it
+as the value for a 'descr' attribute to the GFF record
+.TP
+\fB\-O\fR
+process non\-transcript GFF records as well (by default non\-transcript records are ignored).
+.TP
+\fB\-V\fR
+discard any mRNAs with CDS having in\-frame stop codons
+.TP
+\fB\-H\fR
+for \fB\-V\fR option, check and adjust the starting CDS phase
+if the original phase leads to a translation with an
+in\-frame stop codon
+.TP
+\fB\-B\fR
+for \fB\-V\fR option, single\-exon transcripts are also checked on the
+opposite strand
+.TP
+\fB\-N\fR
+only show multi\-exon mRNAs if all their introns have the
+typical splice site consensus ( GT\-AG, GC\-AG or AT\-AC )
+.TP
+\fB\-M\fR
+discard any mRNAs that either lack initial START codon
+or the terminal STOP codon, or have an in\-frame stop codon
+(only print mRNAs with a fulll, valid CDS)
+.TP
+\fB\-E\fR
+expose (warn about) duplicate transcript IDs and other potential
+problems with the input GFF/GTF records
+.TP
+\fB\-S\fR
+sort output GFF records by genomic sequence and start coordinate
+(this option is automatically enabled by \fB\-g\fR option)
+.TP
+\fB\-Z\fR
+merge close exons into a single exon (for intron size<4)
+.TP
+\fB\-w\fR
+write a fasta file with spliced exons for each GFF transcript
+.TP
+\fB\-x\fR
+write a fasta file with spliced CDS for each GFF transcript
+.TP
+\fB\-W\fR
+for \fB\-w\fR and \fB\-x\fR options, also write for each fasta record the exon
+coordinates projected onto the spliced sequence
+.TP
+\fB\-y\fR
+write a protein fasta file with the translation of CDS for each record
+.TP
+\fB\-o\fR
+the "filtered" GFF records will be written to <outfile.gff>
+(use \fB\-o\-\fR for printing to stdout)
+.TP
+\fB\-t\fR
+use <trackname> in the second column of each GFF output line
+.HP
+\fB\-T\fR \fB\-o\fR option will output GTF format instead of GFF3
+.PP
+Invalid argument: \fB\-\-help\fR
+.PP
+gffread <input_gff> [\-g <genomic_seqs_fasta> | <dir>][\-s <seq_info.fsize>]
+.IP
+[\-o <outfile.gff>] [\-t <tname>] [\-r [[<strand>]<chr>:]<start>..<end>]
+[\-CTVNMAFGRUVBHSZWTOE] [\-w <spl_exons.fa>] [\-x <spl_cds.fa>] [\-y <tr_cds.fa>]
+[\-i <maxintron>]
+Filters and/or converts GFF3/GTF2 records.
+<input_gff> is a GFF file, use '\-' if the GFF records will be given at stdin
+.IP
+Options:
+.TP
+\fB\-g\fR
+full path to a multi\-fasta file with the genomic sequences
+for all input mappings, OR a directory with single\-fasta files
+(one per genomic sequence, with file names matching sequence names)
+.TP
+\fB\-s\fR
+<seq_info.fsize> is a tab\-delimited file providing this info
+for each of the mapped sequences:
+<seq\-name> <seq\-length> <seq\-description>
+(useful for mRNA/EST/protein mappings with \fB\-A\fR option)
+.TP
+\fB\-i\fR
+discard transcripts having an intron larger than <maxintron>
+.TP
+\fB\-r\fR
+only show transcripts crossing coordinate range <start>..<end>
+(on chromosome/contig <chr>, strand <strand> if provided)
+.TP
+\fB\-R\fR
+for \fB\-r\fR option, discard all transcripts that are not fully
+contained within given range
+.TP
+\fB\-U\fR
+discard single\-exon transcripts
+.TP
+\fB\-C\fR
+discard mRNAs that have no CDS feature
+.TP
+\fB\-F\fR
+keep all attributes from last column of GFF/GTF
+.TP
+\fB\-G\fR
+only parse additional exon attributes from the first exon
+and move them to the mRNA level (useful for GTF input)
+.TP
+\fB\-A\fR
+use the description field from <seq_info.fsize> and add it
+as the value for a 'descr' attribute to the GFF record
+.TP
+\fB\-O\fR
+process non\-transcript GFF records as well (by default non\-transcript records are ignored).
+.TP
+\fB\-V\fR
+discard any mRNAs with CDS having in\-frame stop codons
+.TP
+\fB\-H\fR
+for \fB\-V\fR option, check and adjust the starting CDS phase
+if the original phase leads to a translation with an
+in\-frame stop codon
+.TP
+\fB\-B\fR
+for \fB\-V\fR option, single\-exon transcripts are also checked on the
+opposite strand
+.TP
+\fB\-N\fR
+only show multi\-exon mRNAs if all their introns have the
+typical splice site consensus ( GT\-AG, GC\-AG or AT\-AC )
+.TP
+\fB\-M\fR
+discard any mRNAs that either lack initial START codon
+or the terminal STOP codon, or have an in\-frame stop codon
+(only print mRNAs with a fulll, valid CDS)
+.TP
+\fB\-E\fR
+expose (warn about) duplicate transcript IDs and other potential
+problems with the input GFF/GTF records
+.TP
+\fB\-S\fR
+sort output GFF records by genomic sequence and start coordinate
+(this option is automatically enabled by \fB\-g\fR option)
+.TP
+\fB\-Z\fR
+merge close exons into a single exon (for intron size<4)
+.TP
+\fB\-w\fR
+write a fasta file with spliced exons for each GFF transcript
+.TP
+\fB\-x\fR
+write a fasta file with spliced CDS for each GFF transcript
+.TP
+\fB\-W\fR
+for \fB\-w\fR and \fB\-x\fR options, also write for each fasta record the exon
+coordinates projected onto the spliced sequence
+.TP
+\fB\-y\fR
+write a protein fasta file with the translation of CDS for each record
+.TP
+\fB\-o\fR
+the "filtered" GFF records will be written to <outfile.gff>
+(use \fB\-o\-\fR for printing to stdout)
+.TP
+\fB\-t\fR
+use <trackname> in the second column of each GFF output line
+.HP
+\fB\-T\fR \fB\-o\fR option will output GTF format instead of GFF3
+.PP
diff --git a/debian/gtf_to_sam.1 b/debian/gtf_to_sam.1
new file mode 100644
index 0000000..1dfe568
--- /dev/null
+++ b/debian/gtf_to_sam.1
@@ -0,0 +1,14 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4.
+.TH GTF_TO_SAM: "1" "May 2011" "gtf_to_sam v1.0.2" "User Commands"
+.SH NAME
+gtf_to_sam: \- GTF_TO_SAM
+.SH SYNOPSIS
+.B cufflinks
+[\fIoptions\fR] \fI<transcripts1.gtf,\fR...\fI,transcriptsN.gtf> <out.sam>\fR
+gtf_to_sam v1.0.2
+.SH OPTIONS
+\fB\-r\fR/\-\-reference\-seq reference fasta file [ default: NULL ]
+
+\fB\-F\fR/\-\-raw\-fpkm use FPKM instead of isoform fraction
+.PP
+.SH AUTHOR
diff --git a/debian/patches/fix_configure.patch b/debian/patches/fix_configure.patch
new file mode 100644
index 0000000..ae191cd
--- /dev/null
+++ b/debian/patches/fix_configure.patch
@@ -0,0 +1,14 @@
+Description: force configure script to looks for bam.h in /usr/include/samtools
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Last-Update: 2011-05-24
+--- cufflinks-1.0.2.orig/configure
++++ cufflinks-1.0.2/configure
+@@ -4206,7 +4206,7 @@
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h. */
+
+- #include <bam/bam.h>
++ #include <samtools/bam.h>
+
+ int
+ main ()
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
new file mode 100644
index 0000000..dafde04
--- /dev/null
+++ b/debian/patches/fix_includes_path.patch
@@ -0,0 +1,14 @@
+Description: sam.h is located in /usr/include/samtools
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Last-Update: 2011-05-24
+--- cufflinks-1.0.2.orig/src/hits.h
++++ cufflinks-1.0.2/src/hits.h
+@@ -16,7 +16,7 @@
+
+ #include <boost/shared_ptr.hpp>
+
+-#include <bam/sam.h>
++#include <samtools/sam.h>
+
+ #include "common.h"
+ #include "multireads.h"
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..08ef98b
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+fix_includes_path.patch
+fix_configure.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..20fa0b4
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..5e77999
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,9 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+http://cufflinks.cbcb.umd.edu/downloads/cufflinks-([\d\.]*)\.tar\.gz
--
Transcript assembly, differential expression, and differential regulation for RNA-Seq.
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