debian/README.test

-Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by running the provided test:
-
-    sh run-unit-test
-
-in order to confirm its integrity.

debian/changelog

-gffread (0.11.2-1) UNRELEASED; urgency=medium
+gffread (0.11.2-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
-  TODO:
-     https://salsa.debian.org/med-team/gclib
+  * Initial release (Closes: #930545)
 
- -- Andreas Tille <tille@debian.org>  Thu, 18 Apr 2019 12:40:25 +0200
+ -- Andreas Tille <tille@debian.org>  Sat, 15 Jun 2019 00:51:54 +0200

debian/control

@@ -13,6 +13,6 @@ Homepage: https://github.com/gpertea/gffread
 Package: gffread
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction
+Description: GFF/GTF format conversions, region filtering, FASTA sequence extraction
  Gffread is a GFF/GTF parsing utility providing format conversions,
  region filtering, FASTA sequence extraction and more.

debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT

debian/gffread.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH GFFREAD "1" "June 2019" "gffread 0.11.2" "User Commands"
+.SH NAME
+gffread \- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction
+.SH SYNOPSIS
+.B gffread
+<input_gff> [\-g <genomic_seqs_fasta> | <dir>][\-s <seq_info.fsize>]
+[\-o <outfile.gff>] [\-t <tname>] [\-r [[<strand>]<chr>:]<start>..<end> [\-R]]
+[\-CTVNJMKQAFPGUBHZWTOLE] [\-w <exons.fa>] [\-x <cds.fa>] [\-y <tr_cds.fa>]
+[\-i <maxintron>] [\-\-sort\-by <refseq_list.txt>]
+.SH DESCRIPTION
+.IP
+Filter and convert GFF3/GTF2 records, extract corresponding sequences etc.
+By default (i.e. without \fB\-O\fR) only process transcripts, ignore other features.
+.IP
+<input_gff> is a GFF file, use '\-' for stdin
+.SH OPTIONS
+.TP
+\fB\-i\fR
+discard transcripts having an intron larger than <maxintron>
+.TP
+\fB\-l\fR
+discard transcripts shorter than <minlen> bases
+.TP
+\fB\-r\fR
+only show transcripts overlapping 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 the given range
+.TP
+\fB\-U\fR
+discard single\-exon transcripts
+.TP
+\fB\-C\fR
+coding only: discard mRNAs that have no CDS features
+.HP
+\fB\-\-nc\fR non\-coding only: discard mRNAs that have CDS features
+.HP
+\fB\-\-ignore\-locus\fR : discard locus features and attributes found in the 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\-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 \fB\-A\fR option with mRNA/EST/protein mappings)
+.PP
+Sorting: (by default, chromosomes are kept in the order they were found)
+.HP
+\fB\-\-sort\-alpha\fR : chromosomes (reference sequences) are sorted alphabetically
+.HP
+\fB\-\-sort\-by\fR : sort the reference sequences by the order in which their
+.IP
+names are given in the <refseq.lst> file
+.SS "Misc options:"
+.TP
+\fB\-F\fR
+attempt to preserve all GFF attributes preservation
+.HP
+\fB\-\-keep\-exon\-attrs\fR : for \fB\-F\fR option, do not attempt to reduce redundant
+.IP
+exon/CDS attributes
+.TP
+\fB\-G\fR
+do not keep exon attributes, move them to the transcript feature
+(for GFF3 output)
+.HP
+\fB\-\-keep\-genes\fR : in transcript\-only mode (default), also preserve gene records
+.HP
+\fB\-\-keep\-comments\fR: for GFF3 input/output, try to preserve comments
+.TP
+\fB\-O\fR
+process other non\-transcript GFF records (by default non\-transcript
+records are ignored)
+.TP
+\fB\-V\fR
+discard any mRNAs with CDS having in\-frame stop codons (requires \fB\-g\fR)
+.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 (requires \fB\-g\fR)
+.TP
+\fB\-P\fR
+add transcript level GFF attributes about the coding status of each
+transcript, including partialness or in\-frame stop codons (requires \fB\-g\fR)
+.HP
+\fB\-\-add\-hasCDS\fR : add a "hasCDS" attribute with value "true" for transcripts
+.IP
+that have CDS features
+.HP
+\fB\-\-adj\-stop\fR stop codon adjustment: enables \fB\-P\fR and performs automatic
+.IP
+adjustment of the CDS stop coordinate if premature or downstream
+.TP
+\fB\-N\fR
+discard multi\-exon mRNAs that have any intron with a non\-canonical
+splice site consensus (i.e. not GT\-AG, GC\-AG or AT\-AC)
+.TP
+\fB\-J\fR
+discard any mRNAs that either lack initial START codon
+or the terminal STOP codon, or have an in\-frame stop codon
+(i.e. only print mRNAs with a complete CDS)
+.HP
+\fB\-\-no\-pseudo\fR: filter out records matching the 'pseudo' keyword
+.HP
+\fB\-\-in\-bed\fR: input should be parsed as BED format (automatic if the input
+.IP
+filename ends with .bed*)
+.HP
+\fB\-\-in\-tlf\fR: input GFF\-like one\-line\-per\-transcript format without exon/CDS
+.IP
+features (see \fB\-\-tlf\fR option below); automatic if the input
+filename ends with .tlf)
+.SS "Clustering:"
+.HP
+\fB\-M\fR/\-\-merge : cluster the input transcripts into loci, discarding
+.IP
+"duplicated" transcripts (those with the same exact introns
+and fully contained or equal boundaries)
+.HP
+\fB\-d\fR <dupinfo> : for \fB\-M\fR option, write duplication info to file <dupinfo>
+.HP
+\fB\-\-cluster\-only\fR: same as \fB\-M\fR/\-\-merge but without discarding any of the
+.IP
+"duplicate" transcripts, only create "locus" features
+.TP
+\fB\-K\fR
+for \fB\-M\fR option: also discard as redundant the shorter, fully contained
+.IP
+transcripts (intron chains matching a part of the container)
+.TP
+\fB\-Q\fR
+for \fB\-M\fR option, no longer require boundary containment when assessing
+redundancy (can be combined with \fB\-K\fR); only introns have to match for
+multi\-exon transcripts, and >=80% overlap for single\-exon transcripts
+.TP
+\fB\-Y\fR
+for \fB\-M\fR option, enforce \fB\-Q\fR but also discard overlapping single\-exon
+transcripts, even on the opposite strand (can be combined with \fB\-K\fR)
+.SS "Output options:"
+.HP
+\fB\-\-force\-exons\fR: make sure that the lowest level GFF features are considered
+.IP
+"exon" features
+.HP
+\fB\-\-gene2exon\fR: for single\-line genes not parenting any transcripts, add an
+.IP
+exon feature spanning the entire gene (treat it as a transcript)
+.TP
+\fB\-D\fR
+decode url encoded characters within attributes
+.TP
+\fB\-Z\fR
+merge very close exons into a single exon (when intron size<4)
+.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\-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\-y\fR
+write a protein fasta file with the translation of CDS for each record
+.TP
+\fB\-W\fR
+for \fB\-w\fR and \fB\-x\fR options, write in the FASTA defline the exon
+coordinates projected onto the spliced sequence;
+for \fB\-y\fR option, write transcript attributes in the FASTA defline
+.TP
+\fB\-S\fR
+for \fB\-y\fR option, use '*' instead of '.' as stop codon translation
+.TP
+\fB\-L\fR
+Ensembl GTF to GFF3 conversion (implies \fB\-F\fR; should be used with \fB\-m\fR)
+.TP
+\fB\-m\fR
+<chr_replace> is a name mapping table for converting reference
+sequence names, having this 2\-column format:
+<original_ref_ID> <new_ref_ID>
+WARNING: all GFF records on reference sequences whose original IDs
+are not found in the 1st column of this table will be discarded!
+.TP
+\fB\-t\fR
+use <trackname> in the 2nd column of each GFF/GTF output line
+.TP
+\fB\-o\fR
+print the GFF records to <outfile.gff> (those that passed any
+given filters). Use \fB\-o\-\fR to enable printing of to stdout
+.TP
+\fB\-T\fR
+for \fB\-o\fR, output will be GTF instead of GFF3
+.HP
+\fB\-\-bed\fR for \fB\-o\fR, output BED format instead of GFF3
+.HP
+\fB\-\-tlf\fR for \fB\-o\fR, output "transcript line format" which is like GFF
+.IP
+but exons, CDS features and related data are stored as GFF
+attributes in the transcript feature line, like this:
+.IP
+exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
+.IP
+<exons> is a comma\-delimited list of exon_start\-exon_end coordinates;
+<CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>;
+.HP
+\fB\-v\fR,\-E expose (warn about) duplicate transcript IDs and other potential
+.IP
+problems with the given GFF/GTF records
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/install

+gffread	usr/bin

debian/manpages

+debian/*.1

debian/rules

@@ -4,18 +4,8 @@
 export LC_ALL=C.UTF-8
 
 include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
 
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 export GCLDIR=/usr/include/gclib
 

debian/tests/control

-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr

debian/tests/run-unit-test

-#!/bin/bash
-set -e
-
-pkg=#PACKAGENAME#
-
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
-  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  # Double quote below to expand the temporary directory variable now versus
-  # later is on purpose.
-  # shellcheck disable=SC2064
-  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-#do_stuff_to_test_package#