debian/README.Debian

+Since version 2.2.1+dfsg.1-4 the gffread binary is not shipped with cufflinks,
+because up-to-date gffread binary is available via gffread package.
+
+ -- Alex Mestiashvili <mestia@debian.org>  Tue, 20 Aug 2019 17:37:37 +0200

debian/changelog

+cufflinks (2.2.1+dfsg.1-4) unstable; urgency=medium
+
+  [ Valentin Marcon ]
+  * Correct DOI
+
+  [ Alexandre Mestiashvili ]
+  * Drop gffread binary, add gffread package to Recommends in d/control
+    Closes: #934600
+  * Switch to debhelper-compat, bump Policy to 4.4.0, update Uploader's
+    email address
+  * Add README.Debian, explaining why gffread is removed from cufflinks
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Tue, 20 Aug 2019 17:51:28 +0200
+
 cufflinks (2.2.1+dfsg.1-3) unstable; urgency=medium
 
   * XS-Autobuild: yes

debian/compat

-11

debian/control

 Source: cufflinks
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>,
+Uploaders: Alexandre Mestiashvili <mestia@debian.org>,
            Andreas Tille <tille@debian.org>,
            Charles Plessy <plessy@debian.org>
 Section: non-free/science
 XS-Autobuild: yes
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                help2man,
                libboost-dev,
                libboost-serialization-dev,
@@ -16,7 +16,7 @@ Build-Depends: debhelper (>= 11~),
                zlib1g-dev,
                python,
                libeigen3-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/cufflinks
 Vcs-Git: https://salsa.debian.org/med-team/cufflinks.git
 Homepage: http://cufflinks.cbcb.umd.edu
@@ -26,6 +26,7 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          python
+Recommends: gffread
 Enhances: tophat
 Description: Transcript assembly, differential expression and regulation for RNA-Seq
  Cufflinks assembles transcripts, estimates their abundances, and tests for

debian/patches/gffread_show_usage.patch

-From: Alexandre Mestiashvili <alex@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

debian/patches/series

 boost1.65.patch
 fix_gcc-7_ftbfs.patch
-gffread_show_usage.patch
 0004-fix-m64-usage-and-lfs.patch
 0001-fix_spelling.patch
 0002-bam2samtools.patch

debian/rules

@@ -16,6 +16,11 @@ override_dh_auto_clean:
 	dh_auto_clean
 	rm -rf autom4te.cache
 
+override_dh_auto_install:
+	dh_auto_install
+	# skip gffread binary provided by gffread package
+	rm -rf $(bindir)/gffread
+
 override_dh_installman:
 	dh_installman
 
@@ -28,7 +33,3 @@ cuffdiff cuffquant cuffnorm cufflinks ; do \
 	    --version-string="$(DEB_VERSION)" \
 		$(bindir)/$$i > $(mandir)/$$i.1; \
 	done
-	help2man --no-info --no-discard-stderr  \
-	    --name='component of cufflinks suite' \
-	    --version-string="$(DEB_VERSION)" \
-		$(bindir)/gffread > $(mandir)/gffread.1; \