[med-svn] [cufflinks] 06/07: d/patches/gffread_show_usage.patch: fix buffer overflow in gffread d/rules: separate rule for manpage for gffread as it doesn't return usage message when executed without arguments d/*.1: removed obsoleted manpages
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Apr 11 18:58:13 UTC 2014
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository cufflinks.
commit 22f46953208e595535a741edf4f8c9ce9812a0e7
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Apr 11 15:11:40 2014 +0200
d/patches/gffread_show_usage.patch: fix buffer overflow in gffread
d/rules: separate rule for manpage for gffread as it doesn't return usage
message when executed without arguments
d/*.1: removed obsoleted manpages
---
debian/compress_gtf.1 | 19 ---
debian/cuffcompare.1 | 53 -------
debian/cuffdiff.1 | 90 ------------
debian/cufflinks.1 | 240 --------------------------------
debian/cufflinks.manpages | 1 -
debian/cuffmerge.1 | 33 -----
debian/gffread.1 | 219 -----------------------------
debian/gtf_to_sam.1 | 14 --
debian/patches/gffread_show_usage.patch | 154 ++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 7 +-
11 files changed, 161 insertions(+), 670 deletions(-)
diff --git a/debian/compress_gtf.1 b/debian/compress_gtf.1
deleted file mode 100644
index c7a7877..0000000
--- a/debian/compress_gtf.1
+++ /dev/null
@@ -1,19 +0,0 @@
-.\" 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/cuffcompare.1 b/debian/cuffcompare.1
deleted file mode 100644
index 5138968..0000000
--- a/debian/cuffcompare.1
+++ /dev/null
@@ -1,53 +0,0 @@
-.\" 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
deleted file mode 100644
index 734eae6..0000000
--- a/debian/cuffdiff.1
+++ /dev/null
@@ -1,90 +0,0 @@
-.\" 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
deleted file mode 100644
index 3dfe393..0000000
--- a/debian/cufflinks.1
+++ /dev/null
@@ -1,240 +0,0 @@
-.\" 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
deleted file mode 100644
index 0f65186..0000000
--- a/debian/cufflinks.manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/*.1
diff --git a/debian/cuffmerge.1 b/debian/cuffmerge.1
deleted file mode 100644
index c62b971..0000000
--- a/debian/cuffmerge.1
+++ /dev/null
@@ -1,33 +0,0 @@
-.\" 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/gffread.1 b/debian/gffread.1
deleted file mode 100644
index 5499117..0000000
--- a/debian/gffread.1
+++ /dev/null
@@ -1,219 +0,0 @@
-.\" 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
deleted file mode 100644
index 1dfe568..0000000
--- a/debian/gtf_to_sam.1
+++ /dev/null
@@ -1,14 +0,0 @@
-.\" 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/gffread_show_usage.patch b/debian/patches/gffread_show_usage.patch
new file mode 100644
index 0000000..b478b63
--- /dev/null
+++ b/debian/patches/gffread_show_usage.patch
@@ -0,0 +1,154 @@
+From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
+Subject: fix wrong USAGE indentation causing buffer overflow in gffread when
+ using -h, --help and other arguments.
+Forwarded: yes
+--- cufflinks.orig/src/gffread.cpp
++++ cufflinks/src/gffread.cpp
+@@ -12,77 +12,77 @@
+ [-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]\n\
+ [-CTVNJMKQAFGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]\n\
+ [-i <maxintron>] \n\
+- Filters and/or converts GFF3/GTF2 records.\n\
+- <input_gff> is a GFF file, use '-' if the GFF records will be given at stdin\n\
++Filters and/or converts GFF3/GTF2 records.\n\
++<input_gff> is a GFF file, use '-' if the GFF records will be given at stdin\n\
++\n\
++Options:\n\
++ -g full path to a multi-fasta file with the genomic sequences\n\
++ for all input mappings, OR a directory with single-fasta files\n\
++ (one per genomic sequence, with file names matching sequence names)\n\
++ -s <seq_info.fsize> is a tab-delimited file providing this info\n\
++ for each of the mapped sequences:\n\
++ <seq-name> <seq-length> <seq-description>\n\
++ (useful for -A option with mRNA/EST/protein mappings)\n\
++ -i discard transcripts having an intron larger than <maxintron>\n\
++ -r only show transcripts overlapping coordinate range <start>..<end>\n\
++ (on chromosome/contig <chr>, strand <strand> if provided)\n\
++ -R for -r option, discard all transcripts that are not fully \n\
++ contained within the given range\n\
++ -U discard single-exon transcripts\n\
++ -C coding only: discard mRNAs that have no CDS feature\n\
++ -F full GFF attribute preservation (all attributes are shown)\n\
++ -G only parse additional exon attributes from the first exon\n\
++ and move them to the mRNA level (useful for GTF input)\n\
++ -A use the description field from <seq_info.fsize> and add it\n\
++ as the value for a 'descr' attribute to the GFF record\n\
+ \n\
+- Options:\n\
+- -g full path to a multi-fasta file with the genomic sequences\n\
+- for all input mappings, OR a directory with single-fasta files\n\
+- (one per genomic sequence, with file names matching sequence names)\n\
+- -s <seq_info.fsize> is a tab-delimited file providing this info\n\
+- for each of the mapped sequences:\n\
+- <seq-name> <seq-length> <seq-description>\n\
+- (useful for -A option with mRNA/EST/protein mappings)\n\
+- -i discard transcripts having an intron larger than <maxintron>\n\
+- -r only show transcripts overlapping coordinate range <start>..<end>\n\
+- (on chromosome/contig <chr>, strand <strand> if provided)\n\
+- -R for -r option, discard all transcripts that are not fully \n\
+- contained within the given range\n\
+- -U discard single-exon transcripts\n\
+- -C coding only: discard mRNAs that have no CDS feature\n\
+- -F full GFF attribute preservation (all attributes are shown)\n\
+- -G only parse additional exon attributes from the first exon\n\
+- and move them to the mRNA level (useful for GTF input)\n\
+- -A use the description field from <seq_info.fsize> and add it\n\
+- as the value for a 'descr' attribute to the GFF record\n\
+- \n\
+- -O process also non-transcript GFF records (by default non-transcript\n\
+- records are ignored)\n\
+- -V discard any mRNAs with CDS having in-frame stop codons\n\
+- -H for -V option, check and adjust the starting CDS phase\n\
+- if the original phase leads to a translation with an \n\
+- in-frame stop codon\n\
+- -B for -V option, single-exon transcripts are also checked on the\n\
+- opposite strand\n\
+- -N discard multi-exon mRNAs that have any intron with a non-canonical\n\
+- splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)\n\
+- -J discard any mRNAs that either lack initial START codon\n\
+- or the terminal STOP codon, or have an in-frame stop codon\n\
+- (only print mRNAs with a fulll, valid CDS)\n\
+- --no-pseudo: filter out records matching the 'pseudo' keyword\n\
+- \n\
+- -M/--merge : cluster the input transcripts into loci, collapsing matching\n\
+- transcripts (those with the same exact introns and fully contained)\n\
+- -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>\n\
+- --cluster-only: same as --merge but without collapsing matching transcripts\n\
+- -K for -M option: also collapse shorter, fully contained transcripts\n\
+- with fewer introns than the container\n\
+- -Q for -M option, remove the containment restriction:\n\
+- (multi-exon transcripts will be collapsed if just their introns match,\n\
+- while single-exon transcripts can partially overlap (80%))\n\
+- \n\
+- --force-exons: make sure that the lowest level GFF features are printed as \n\
+- \"exon\" features\n\
+- -E expose (warn about) duplicate transcript IDs and other potential \n\
+- problems with the given GFF/GTF records\n\
+- -D decode url encoded characters within attributes\n\
+- -Z merge close exons into a single exon (for intron size<4)\n\
+- -w write a fasta file with spliced exons for each GFF transcript\n\
+- -x write a fasta file with spliced CDS for each GFF transcript\n\
+- -W for -w and -x options, also write for each fasta record the exon\n\
+- coordinates projected onto the spliced sequence\n\
+- -y write a protein fasta file with the translation of CDS for each record\n\
+- -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)\n\
+- -m <chr_replace> is a reference (genomic) sequence replacement table with\n\
+- this format:\n\
+- <original_ref_ID> <new_ref_ID>\n\
+- GFF records on reference sequences that are not found among the\n\
+- <original_ref_ID> entries in this file will be filtered out\n\
+- -o the \"filtered\" GFF records will be written to <outfile.gff>\n\
+- (use -o- for printing to stdout)\n\
+- -t use <trackname> in the second column of each GFF output line\n\
+- -T -o option will output GTF format instead of GFF3\n\
+- "
++ -O process also non-transcript GFF records (by default non-transcript\n\
++ records are ignored)\n\
++ -V discard any mRNAs with CDS having in-frame stop codons\n\
++ -H for -V option, check and adjust the starting CDS phase\n\
++ if the original phase leads to a translation with an \n\
++ in-frame stop codon\n\
++ -B for -V option, single-exon transcripts are also checked on the\n\
++ opposite strand\n\
++ -N discard multi-exon mRNAs that have any intron with a non-canonical\n\
++ splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)\n\
++ -J discard any mRNAs that either lack initial START codon\n\
++ or the terminal STOP codon, or have an in-frame stop codon\n\
++ (only print mRNAs with a fulll, valid CDS)\n\
++ --no-pseudo: filter out records matching the 'pseudo' keyword\n\
++\n\
++ -M/--merge : cluster the input transcripts into loci, collapsing matching\n\
++ transcripts (those with the same exact introns and fully contained)\n\
++ -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>\n\
++ --cluster-only: same as --merge but without collapsing matching transcripts\n\
++ -K for -M option: also collapse shorter, fully contained transcripts\n\
++ with fewer introns than the container\n\
++ -Q for -M option, remove the containment restriction:\n\
++ (multi-exon transcripts will be collapsed if just their introns match,\n\
++ while single-exon transcripts can partially overlap (80%))\n\
++\n\
++ --force-exons: make sure that the lowest level GFF features are printed as \n\
++ \"exon\" features\n\
++ -E expose (warn about) duplicate transcript IDs and other potential \n\
++ problems with the given GFF/GTF records\n\
++ -D decode url encoded characters within attributes\n\
++ -Z merge close exons into a single exon (for intron size<4)\n\
++ -w write a fasta file with spliced exons for each GFF transcript\n\
++ -x write a fasta file with spliced CDS for each GFF transcript\n\
++ -W for -w and -x options, also write for each fasta record the exon\n\
++ coordinates projected onto the spliced sequence\n\
++ -y write a protein fasta file with the translation of CDS for each record\n\
++ -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)\n\
++ -m <chr_replace> is a reference (genomic) sequence replacement table with\n\
++ this format:\n\
++ <original_ref_ID> <new_ref_ID>\n\
++ GFF records on reference sequences that are not found among the\n\
++ <original_ref_ID> entries in this file will be filtered out\n\
++ -o the \"filtered\" GFF records will be written to <outfile.gff>\n\
++ (use -o- for printing to stdout)\n\
++ -t use <trackname> in the second column of each GFF output line\n\
++ -T -o option will output GTF format instead of GFF3\n\
++"
+
+
+ class SeqInfo { //populated from the -s option of gffread
diff --git a/debian/patches/series b/debian/patches/series
index 805bdd1..fe10689 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+gffread_show_usage.patch
0004-fix-m64-usage-and-lfs.patch
0001-fix_spelling.patch
0002-bam2samtools.patch
diff --git a/debian/rules b/debian/rules
index 99d94cb..e62c981 100755
--- a/debian/rules
+++ b/debian/rules
@@ -27,11 +27,16 @@ override_dh_installman:
# try to create man pages whereever possible
mkdir -p $(mandir)
- for i in cuffcompare compress_gtf gffread gtf_to_sam cuffmerge \
+ for i in cuffcompare compress_gtf gtf_to_sam cuffmerge \
cuffdiff cuffquant cuffnorm cufflinks ; do \
help2man --no-info --no-discard-stderr -h "" \
--name='cufflinks suite component' \
--version-string="$(version)" \
$(bindir)/$$i > $(mandir)/$$i.1; \
done
+ help2man --no-info --no-discard-stderr \
+ --name='cufflinks suite component' \
+ --version-string="$(version)" \
+ $(bindir)/gffread > $(mandir)/gffread.1; \
+
--
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