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commit 22f46953208e595535a741edf4f8c9ce9812a0e7 Author: Alexandre Mestiashvili <[email protected]> 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 <[email protected]> +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; \ + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cufflinks.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
