[med-svn] [fastaq_tmp] 03/03: Add debian/ dir as uploaded for version 1.6.0 which magically vanished after `git import-orig`. Seems this repository remains broken. :-(
Andreas Tille
tille at debian.org
Tue Mar 3 07:44:53 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fastaq_tmp.
commit a87529d9d45d0df82e5b758d9bb52ed3b0417171
Author: Andreas Tille <tille at debian.org>
Date: Tue Mar 3 08:43:37 2015 +0100
Add debian/ dir as uploaded for version 1.6.0 which magically vanished after `git import-orig`. Seems this repository remains broken. :-(
---
debian/changelog | 11 +
debian/compat | 1 +
debian/control | 169 +++++
debian/copyright | 22 +
debian/fastaq.manpages | 1 +
...ay-import-statements-for-manpage-creation.patch | 774 +++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 25 +
debian/source/format | 1 +
debian/upstream/metadata | 12 +
debian/usage_to_man | 142 ++++
debian/watch | 3 +
12 files changed, 1162 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..89a691d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,11 @@
+fastaq (1.6.0-1) experimental; urgency=medium
+
+ * New upstream release
+
+ -- Jorge Soares <j.s.soares at gmail.com> Tue, 18 Nov 2014 16:34:01 +0000
+
+fastaq (1.5.0-1) unstable; urgency=medium
+
+ * Initial release (Closes: #766321)
+
+ -- Jorge Soares <j.s.soares at gmail.com> Thu, 23 Oct 2014 20:23:54 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..e5d6731
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,169 @@
+Source: fastaq
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Jorge Soares <j.s.soares at gmail.com>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ python3,
+ python3-setuptools,
+ python3-numpy,
+ python3-nose,
+ samtools,
+ help2man
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git
+Homepage: https://github.com/sanger-pathogens/Fastaq
+
+Package: fastaq
+Architecture: all
+Depends: ${python3:Depends},
+ ${misc:Depends}
+Description: FASTA and FASTQ file manipulation tools
+ A collection of scripts that perform useful and common
+ fasta/q manipulation tasks.
+ .
+ All scripts automatically detect whether the input is
+ a FASTA or FASTQ file.
+ .
+ Input and output files can be gzipped.
+ .
+ fastaq_capillary_to_pairs -
+ Given a fasta/q file of capillary reads,
+ makes an interleaved file of read pairs
+ .
+ fastaq_chunker -
+ Splits a multi fasta/q file into separate files.
+ Splits sequences into chunks of a fixed size.
+ .
+ fastaq_count_sequences -
+ Counts the number of sequences in a fasta/q file
+ .
+ fastaq_deinterleave -
+ Deinterleaves fasta/q file, so that reads are written
+ alternately between two output files
+ .
+ fastaq_enumerate_names -
+ Renames sequences in a file, calling them 1,2,3...
+ .
+ fastaq_expand_nucleotides -
+ Makes all combinations of sequences in input file
+ by using all possibilities of redundant bases.
+ e.g. ART could be AAT or AGT.
+ .
+ fastaq_extend_gaps -
+ Extends the length of all gaps (and trims the start/end
+ of sequences) in a fasta/q file.
+ .
+ fastaq_fasta_to_fastq -
+ Given a fasta and qual file, makes a fastq file.
+ .
+ fastaq_filter -
+ Filters a fasta/q file by sequence length and/or
+ by name matching a regular expression.
+ .
+ fastaq_get_ids -
+ Gets IDs from each sequence in a fasta or fastq file.
+ .
+ fastaq_get_seq_flanking_gaps -
+ Gets the sequences either side of gaps in a fasta/q file.
+ .
+ fastaq_insert_or_delete_bases -
+ Deletes or inserts bases at given position(s)
+ from a fasta/q file.
+ .
+ fastaq_interleave -
+ Interleaves two fasta/q files, so that reads are written
+ alternately first/second in output file.
+ .
+ fastaq_long_read_simulate -
+ Simulates long reads from a fasta/q file. Can optionally
+ make insertions into the reads, like pacbio does.
+ .
+ fastaq_make_random_contigs -
+ Makes a multi-fasta file of random sequences,
+ all of the same length. Each base has equal chance of
+ being A,C,G or T
+ .
+ fastaq_merge -
+ Converts multi fasta/q file to single sequence file,
+ preserving original order of sequences.
+ .
+ fastaq_replace_bases -
+ Replaces all occurences of one letter with another in
+ a fasta/q file.
+ .
+ fastaq_reverse_complement -
+ Reverse complements all sequences in a fasta/q file
+ .
+ fastaq_scaffolds_to_contigs -
+ Creates a file of contigs from a file of scaffolds - i.e.
+ breaks at every gap in the input.
+ .
+ fastaq_search_for_seq -
+ Searches for an exact match on a given string and its
+ reverese complement, in every sequences of a fasta/q file.
+ Case insensitive. Guaranteed to find all hits.
+ .
+ fastaq_sequence_trim -
+ Trims sequences off the start of all sequences in a pair
+ of fasta/q files, whenever there is a perfect match.
+ Only keeps a read pair if both reads of the pair are at
+ least a minimum length after any trimming.
+ .
+ fastaq_split_by_base_count -
+ Splits a multi fasta/q file into separate files.
+ Does not split sequences. Puts up to max_bases
+ into each split file. The exception is that any
+ sequence longer than max_bases is put into its own file.
+ .
+ fastaq_strip_illumina_suffix -
+ Strips /1 or /2 off the end of every read name
+ in a fasta/q file.
+ .
+ fastaq_to_fake_qual -
+ Makes fake quality scores file from a fasta/q file.
+ .
+ fastaq_to_fasta -
+ Converts sequence file to FASTA format.
+ .
+ fastaq_to_mira_xml -
+ Creates an xml file from a fasta/q file of reads,
+ for use with Mira assembler.
+ .
+ fastaq_to_orfs_gff -
+ Writes a GFF file of open reading frames from a fasta/q file
+ .
+ fastaq_to_perfect_reads -
+ Makes perfect paired end fastq reads from a fasta/q file,
+ with insert sizes sampled from a normal distribution.
+ Read orientation is innies. Output is an interleaved fastq file.
+ .
+ fastaq_to_random_subset -
+ Takes a random subset of reads from a fasta/q file and optionally
+ the corresponding read from a mates file.
+ Ouptut is interleaved if mates file given.
+ .
+ fastaq_to_tiling_bam -
+ Takes a fasta/q file. Makes a BAM file containing perfect
+ (unpaired) reads tiling the whole genome.
+ .
+ fastaq_to_unique_by_id -
+ Removes duplicate sequences from a fasta/q file,
+ based on their names. If the same name is found
+ more than once, then the longest sequence is kept.
+ Order of sequences is preserved in output.
+ .
+ fastaq_translate -
+ Translates all sequences in a fasta or fastq file.
+ Output is always fasta format
+ .
+ fastaq_trim_ends -
+ Trims set number of bases off each sequence in a fasta/q file
+ .
+ fastaq_trim_Ns_at_end -
+ Trims any Ns off each sequence in a fasta/q file.
+ Does nothing to gaps in the middle, just trims the ends
+ .
+ A developer API is also provided by this package.
+ There are plenty of examples in tasks.py
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ca8eea8
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,22 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Fastaq
+Source: https://github.com/sanger-pathogens/Fastaq
+
+Files: *
+Copyright: © 2012-2013 Martin Hunt <mh12 at sanger.ac.uk>
+License: GPL-3
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/fastaq.manpages b/debian/fastaq.manpages
new file mode 100644
index 0000000..d2c65e3
--- /dev/null
+++ b/debian/fastaq.manpages
@@ -0,0 +1 @@
+debian/man/*
\ No newline at end of file
diff --git a/debian/patches/delay-import-statements-for-manpage-creation.patch b/debian/patches/delay-import-statements-for-manpage-creation.patch
new file mode 100644
index 0000000..48dac81
--- /dev/null
+++ b/debian/patches/delay-import-statements-for-manpage-creation.patch
@@ -0,0 +1,774 @@
+Description: Delay import of Fastaq modules by the python executables
+ Man pages for this package are being automatically created with through the
+ help2man wrapper called usage_to_man. help2man calls the python executables
+ with the -h option and converts the usage into a man page.
+ .
+ The first step done by all the executables is the import of the modules deployed
+ by this package. Since the package is not installed in the system at build time,
+ the man pages would never be properly created.
+ .
+ This patch solves this problem by importing the modules in this package after
+ the argument parsing code.
+ .
+ Upstream prefered to keep the code as it is for styling reasons, which is
+ perfectly reasonable
+ .
+ fastaq (1.5.0-1) UNRELEASED; urgency=low
+ .
+ * Initial release (Closes: #766321)
+Author: Jorge Soares <j.s.soares at gmail.com>
+Index: fastaq/scripts/fastaq_capillary_to_pairs
+===================================================================
+--- fastaq.orig/scripts/fastaq_capillary_to_pairs
++++ fastaq/scripts/fastaq_capillary_to_pairs
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Given a fasta/q file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2',
+@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outprefix', help='Prefix of output files', metavar='outfiles prefix')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.capillary_to_pairs(options.infile, options.outprefix)
+Index: fastaq/scripts/fastaq_chunker
+===================================================================
+--- fastaq.orig/scripts/fastaq_chunker
++++ fastaq/scripts/fastaq_chunker
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Splits a multi fasta/q file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk_size chunks in each file, but allows a little extra, so chunk can be up to (chunk_size + tolerance), to prevent tiny chunks made from the ends of sequences',
+@@ -12,6 +11,10 @@ parser.add_argument('chunk_size', type=i
+ parser.add_argument('tolerance', type=int, help='Tolerance allowed in chunk size')
+ parser.add_argument('--skip_all_Ns', action='store_true', help='Do not output any sequence that consists of all Ns')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.split_by_fixed_size(
+ options.infile,
+ options.outprefix,
+Index: fastaq/scripts/fastaq_count_sequences
+===================================================================
+--- fastaq.orig/scripts/fastaq_count_sequences
++++ fastaq/scripts/fastaq_count_sequences
+@@ -1,11 +1,14 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Counts the number of sequences in a fasta/q file',
+ usage = '%(prog)s <fasta/q in>')
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ print(tasks.count_sequences(options.infile))
+Index: fastaq/scripts/fastaq_deinterleave
+===================================================================
+--- fastaq.orig/scripts/fastaq_deinterleave
++++ fastaq/scripts/fastaq_deinterleave
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Deinterleaves fasta/q file, so that reads are written alternately between two output files',
+@@ -11,4 +10,8 @@ parser.add_argument('infile', help='Name
+ parser.add_argument('out_fwd', help='Name of output fasta/q file of forwards reads')
+ parser.add_argument('out_rev', help='Name of output fasta/q file of reverse reads')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.deinterleave(options.infile, options.out_fwd, options.out_rev, fasta_out=options.fasta_out)
+Index: fastaq/scripts/fastaq_enumerate_names
+===================================================================
+--- fastaq.orig/scripts/fastaq_enumerate_names
++++ fastaq/scripts/fastaq_enumerate_names
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Renames sequences in a file, calling them 1,2,3... etc',
+@@ -12,6 +11,10 @@ parser.add_argument('--keep_suffix', act
+ parser.add_argument('infile', help='Name of fasta/q file to be read')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.enumerate_names(options.infile,
+ options.outfile,
+ start_index=options.start_index,
+Index: fastaq/scripts/fastaq_expand_nucleotides
+===================================================================
+--- fastaq.orig/scripts/fastaq_expand_nucleotides
++++ fastaq/scripts/fastaq_expand_nucleotides
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. Assumes input is nucleotides, not amino acids',
+@@ -9,6 +8,10 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input file. Can be any of FASTA, FASTQ, GFF3, EMBL, GBK, Phylip')
+ parser.add_argument('outfile', help='Name of output file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.expand_nucleotides(
+ options.infile,
+ options.outfile,
+Index: fastaq/scripts/fastaq_extend_gaps
+===================================================================
+--- fastaq.orig/scripts/fastaq_extend_gaps
++++ fastaq/scripts/fastaq_extend_gaps
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. Does this by replacing a set number of bases either side of each gap with Ns. Any sequence that ends up as all Ns is lost',
+@@ -10,4 +9,8 @@ parser.add_argument('--trim_number', typ
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.extend_gaps(options.infile, options.outfile, options.trim_number)
+Index: fastaq/scripts/fastaq_fasta_to_fastq
+===================================================================
+--- fastaq.orig/scripts/fastaq_fasta_to_fastq
++++ fastaq/scripts/fastaq_fasta_to_fastq
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Given a fasta and qual file, makes a fastq file',
+@@ -10,4 +9,8 @@ parser.add_argument('fasta', help='Name
+ parser.add_argument('qual', help='Name of input quality scores file', metavar='qual in')
+ parser.add_argument('outfile', help='Name of output fastq file', metavar='fastq out')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.fasta_to_fastq(options.fasta, options.qual, options.outfile)
+Index: fastaq/scripts/fastaq_filter
+===================================================================
+--- fastaq.orig/scripts/fastaq_filter
++++ fastaq/scripts/fastaq_filter
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Filters a fasta/q file by sequence length and/or by name matching a regular expression',
+@@ -14,6 +13,10 @@ parser.add_argument('-v', '--invert', ac
+ parser.add_argument('infile', help='Name of fasta/q file to be filtered')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.filter(options.infile,
+ options.outfile,
+ minlength=options.min_length,
+Index: fastaq/scripts/fastaq_get_ids
+===================================================================
+--- fastaq.orig/scripts/fastaq_get_ids
++++ fastaq/scripts/fastaq_get_ids
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Gets IDs from each sequence in a fasta or fastq file',
+@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.get_ids(options.infile, options.outfile)
+Index: fastaq/scripts/fastaq_get_seq_flanking_gaps
+===================================================================
+--- fastaq.orig/scripts/fastaq_get_seq_flanking_gaps
++++ fastaq/scripts/fastaq_get_seq_flanking_gaps
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Gets the sequences either side of gaps in a fasta/q file',
+@@ -11,4 +10,8 @@ parser.add_argument('--right', type=int,
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.get_seqs_flanking_gaps(options.infile, options.outfile, options.left, options.right)
+Index: fastaq/scripts/fastaq_insert_or_delete_bases
+===================================================================
+--- fastaq.orig/scripts/fastaq_insert_or_delete_bases
++++ fastaq/scripts/fastaq_insert_or_delete_bases
+@@ -1,9 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-import sys
+-import random
+-from fastaq import sequences, utils, intervals
+
+ parser = argparse.ArgumentParser(
+ description = 'Deletes or inserts bases at given position(s) from a fasta/q file',
+@@ -16,6 +13,11 @@ parser.add_argument('-i','--insert', act
+ parser.add_argument('--insert_range', help='Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)*step bases into sequence n.', metavar='P,start,step')
+ options = parser.parse_args()
+
++
++import sys
++import random
++from fastaq import sequences, utils, intervals
++
+ test_ops = [int(x is not None) for x in [options.delete, options.insert, options.delete_range, options.insert_range]]
+
+ if sum(test_ops) != 1:
+Index: fastaq/scripts/fastaq_interleave
+===================================================================
+--- fastaq.orig/scripts/fastaq_interleave
++++ fastaq/scripts/fastaq_interleave
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Interleaves two fasta/q files, so that reads are written alternately first/second in output file',
+@@ -10,4 +9,8 @@ parser.add_argument('infile_1', help='Na
+ parser.add_argument('infile_2', help='Name of second input fasta/q file')
+ parser.add_argument('outfile', help='Name of output fasta/q file of interleaved reads')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.interleave(options.infile_1, options.infile_2, options.outfile)
+Index: fastaq/scripts/fastaq_long_read_simulate
+===================================================================
+--- fastaq.orig/scripts/fastaq_long_read_simulate
++++ fastaq/scripts/fastaq_long_read_simulate
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. If insertions made, coverage calculation is done before the insertions (so total read length may appear longer then expected).',
+@@ -29,8 +28,11 @@ ins_group = parser.add_argument_group('o
+ ins_group.add_argument('--ins_skip', type=int, help='Insert a random base every --skip bases plus or minus --ins_window. If this option is used, must also use --ins_window.', metavar='INT')
+ ins_group.add_argument('--ins_window', type=int, help='See --ins_skip. If this option is used, must also use --ins_skip.', metavar='INT')
+
+-
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.make_long_reads(
+ options.infile,
+ options.outfile,
+Index: fastaq/scripts/fastaq_make_random_contigs
+===================================================================
+--- fastaq.orig/scripts/fastaq_make_random_contigs
++++ fastaq/scripts/fastaq_make_random_contigs
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Makes a multi-fasta file of random sequences, all of the same length. Each base has equal chance of being A,C,G or T',
+@@ -14,6 +13,10 @@ parser.add_argument('contigs', type=int,
+ parser.add_argument('length', type=int, help='Length of each contig')
+ parser.add_argument('outfile', help='Name of output file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.make_random_contigs(
+ options.contigs,
+ options.length,
+Index: fastaq/scripts/fastaq_merge
+===================================================================
+--- fastaq.orig/scripts/fastaq_merge
++++ fastaq/scripts/fastaq_merge
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Converts multi fasta/q file to single sequence file, preserving original order of sequences',
+@@ -10,6 +9,10 @@ parser.add_argument('infile', help='Name
+ parser.add_argument('outfile', help='Name of output file')
+ parser.add_argument('-n', '--name', help='Name of sequence in output file [%(default)s]', default='union')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.merge_to_one_seq(
+ options.infile,
+ options.outfile,
+Index: fastaq/scripts/fastaq_replace_bases
+===================================================================
+--- fastaq.orig/scripts/fastaq_replace_bases
++++ fastaq/scripts/fastaq_replace_bases
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Replaces all occurences of one letter with another in a fasta/q file',
+@@ -11,4 +10,8 @@ parser.add_argument('outfile', help='Nam
+ parser.add_argument('old', help='Base to be replaced')
+ parser.add_argument('new', help='Replace with this letter')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.replace_bases(options.infile, options.outfile, options.old, options.new)
+Index: fastaq/scripts/fastaq_reverse_complement
+===================================================================
+--- fastaq.orig/scripts/fastaq_reverse_complement
++++ fastaq/scripts/fastaq_reverse_complement
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Reverse complements all sequences in a fasta/q file',
+@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.reverse_complement(options.infile, options.outfile)
+Index: fastaq/scripts/fastaq_scaffolds_to_contigs
+===================================================================
+--- fastaq.orig/scripts/fastaq_scaffolds_to_contigs
++++ fastaq/scripts/fastaq_scaffolds_to_contigs
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input',
+@@ -10,4 +9,7 @@ parser.add_argument('--number_contigs',
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output contigs file')
+ options = parser.parse_args()
++
++from fastaq import tasks
++
+ tasks.scaffolds_to_contigs(options.infile, options.outfile, number_contigs=options.number_contigs)
+Index: fastaq/scripts/fastaq_search_for_seq
+===================================================================
+--- fastaq.orig/scripts/fastaq_search_for_seq
++++ fastaq/scripts/fastaq_search_for_seq
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Searches for an exact match on a given string and its reverese complement, in every sequences of a fasta/q file. Case insensitive. Guaranteed to find all hits',
+@@ -10,4 +9,7 @@ parser.add_argument('infile', help='Name
+ parser.add_argument('outfile', help='Name of outputfile. Tab-delimited output: sequence name, position, strand')
+ parser.add_argument('search_string', help='String to search for in the sequences')
+ options = parser.parse_args()
++
++from fastaq import tasks
++
+ tasks.search_for_seq(options.infile, options.outfile, options.search_string)
+Index: fastaq/scripts/fastaq_sequence_trim
+===================================================================
+--- fastaq.orig/scripts/fastaq_sequence_trim
++++ fastaq/scripts/fastaq_sequence_trim
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming',
+@@ -14,6 +13,10 @@ parser.add_argument('outfile_1', help='N
+ parser.add_argument('outfile_2', help='Name of output reverse fasta/q file', metavar='out_2')
+ parser.add_argument('trim_seqs', help='Name of fasta/q file of sequences to search for at the start of each input sequence', metavar='trim_seqs')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.sequence_trim(
+ options.infile_1,
+ options.infile_2,
+Index: fastaq/scripts/fastaq_split_by_base_count
+===================================================================
+--- fastaq.orig/scripts/fastaq_split_by_base_count
++++ fastaq/scripts/fastaq_split_by_base_count
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Splits a multi fasta/q file into separate files. Does not split sequences. Puts up to max_bases into each split file. The exception is that any sequence longer than max_bases is put into its own file.',
+@@ -12,4 +11,8 @@ parser.add_argument('max_bases', type=in
+ parser.add_argument('--max_seqs', type=int, help='Max number of sequences in each output split file [no limit]', metavar='INT')
+
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.split_by_base_count(options.infile, options.outprefix, options.max_bases, options.max_seqs)
+Index: fastaq/scripts/fastaq_strip_illumina_suffix
+===================================================================
+--- fastaq.orig/scripts/fastaq_strip_illumina_suffix
++++ fastaq/scripts/fastaq_strip_illumina_suffix
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Strips /1 or /2 off the end of every read name in a fasta/q file',
+@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.strip_illumina_suffix(options.infile, options.outfile)
+Index: fastaq/scripts/fastaq_to_fake_qual
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_fake_qual
++++ fastaq/scripts/fastaq_to_fake_qual
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Makes fake quality scores file from a fasta/q file',
+@@ -10,6 +9,10 @@ parser.add_argument('infile', help='Name
+ parser.add_argument('outfile', help='Name of output file')
+ parser.add_argument('-q', '--qual', type=int, help='Quality score to assign to all bases [%(default)s]', default=40)
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.fastaq_to_fake_qual(
+ options.infile,
+ options.outfile,
+Index: fastaq/scripts/fastaq_to_fasta
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_fasta
++++ fastaq/scripts/fastaq_to_fasta
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Converts sequence file to FASTA format',
+@@ -11,6 +10,10 @@ parser.add_argument('outfile', help='Nam
+ parser.add_argument('-l', '--line_length', type=int, help='Number of bases on each sequence line of output file [%(default)s]', default=60)
+ parser.add_argument('-s', '--strip_after_whitespace', action='store_true', help='Remove everything after first whitesapce in every sequence name')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.to_fasta(
+ options.infile,
+ options.outfile,
+Index: fastaq/scripts/fastaq_to_mira_xml
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_mira_xml
++++ fastaq/scripts/fastaq_to_mira_xml
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Creates an xml file from a fasta/q file of reads, for use with Mira assembler',
+@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('xml_out', help='Name of output xml file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.fastaq_to_mira_xml(options.infile, options.xml_out)
+Index: fastaq/scripts/fastaq_to_orfs_gff
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_orfs_gff
++++ fastaq/scripts/fastaq_to_orfs_gff
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Writes a GFF file of open reading frames from a fasta/q file',
+@@ -10,4 +9,8 @@ parser.add_argument('--min_length', type
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('gff_out', help='Name of output gff file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.fastaq_to_orfs_gff(options.infile, options.gff_out, min_length=options.min_length)
+Index: fastaq/scripts/fastaq_to_perfect_reads
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_perfect_reads
++++ fastaq/scripts/fastaq_to_perfect_reads
+@@ -1,10 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-import random
+-from math import floor, ceil
+-from fastaq import sequences, utils
+-import sys
+
+ parser = argparse.ArgumentParser(
+ description = 'Makes perfect paired end fastq reads from a fasta/q file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved fastq file.',
+@@ -20,6 +16,12 @@ parser.add_argument('--no_n', action='st
+ parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None, metavar='INT')
+ options = parser.parse_args()
+
++
++import random
++from math import floor, ceil
++from fastaq import sequences, utils
++import sys
++
+ random.seed(a=options.seed)
+
+ seq_reader = sequences.file_reader(options.infile)
+Index: fastaq/scripts/fastaq_to_random_subset
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_random_subset
++++ fastaq/scripts/fastaq_to_random_subset
+@@ -1,9 +1,6 @@
+ #!/usr/bin/env python3
+
+-import sys
+ import argparse
+-import random
+-from fastaq import sequences, utils
+
+ parser = argparse.ArgumentParser(
+ description = 'Takes a random subset of reads from a fasta/q file and optionally the corresponding read ' +
+@@ -15,6 +12,11 @@ parser.add_argument('outfile', help='Nam
+ parser.add_argument('probability', type=int, help='Probability of keeping any given read (pair) in [0,100]', metavar='INT')
+ options = parser.parse_args()
+
++
++import sys
++import random
++from fastaq import sequences, utils
++
+ seq_reader = sequences.file_reader(options.infile)
+ fout = utils.open_file_write(options.outfile)
+
+Index: fastaq/scripts/fastaq_to_tiling_bam
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_tiling_bam
++++ fastaq/scripts/fastaq_to_tiling_bam
+@@ -1,9 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-import sys
+-import os
+-from fastaq import sequences, utils
+
+ parser = argparse.ArgumentParser(
+ description = 'Takes a fasta/q file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome',
+@@ -17,6 +14,11 @@ parser.add_argument('outfile', help='Nam
+ parser.add_argument('--read_group', help='Add the given read group ID to all reads [%(default)s]' ,default='42')
+ options = parser.parse_args()
+
++
++import sys
++import os
++from fastaq import sequences, utils
++
+ # make a header first - we need to add the @RG line to the default header made by samtools
+ tmp_empty_file = options.outfile + '.tmp.empty'
+ f = utils.open_file_write(tmp_empty_file)
+Index: fastaq/scripts/fastaq_to_unique_by_id
+===================================================================
+--- fastaq.orig/scripts/fastaq_to_unique_by_id
++++ fastaq/scripts/fastaq_to_unique_by_id
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Removes duplicate sequences from a fasta/q file, based on their names. If the same name is found more than once, then the longest sequence is kept. Order of sequences is preserved in output',
+@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.to_unique_by_id(options.infile, options.outfile)
+Index: fastaq/scripts/fastaq_translate
+===================================================================
+--- fastaq.orig/scripts/fastaq_translate
++++ fastaq/scripts/fastaq_translate
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Translates all sequences in a fasta or fastq file. Output is always fasta format',
+@@ -10,4 +9,8 @@ parser.add_argument('--frame', type=int,
+ parser.add_argument('infile', help='Name of fasta/q file to be translated', metavar='in.fasta/q')
+ parser.add_argument('outfile', help='Name of output fasta file', metavar='out.fasta')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.translate(options.infile, options.outfile, frame=options.frame)
+Index: fastaq/scripts/fastaq_trim_Ns_at_end
+===================================================================
+--- fastaq.orig/scripts/fastaq_trim_Ns_at_end
++++ fastaq/scripts/fastaq_trim_Ns_at_end
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Trims any Ns off each sequence in a fasta/q file. Does nothing to gaps in the middle, just trims the ends',
+@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(
+ parser.add_argument('infile', help='Name of input fasta/q file')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.trim_Ns_at_end(options.infile, options.outfile)
+Index: fastaq/scripts/fastaq_trim_ends
+===================================================================
+--- fastaq.orig/scripts/fastaq_trim_ends
++++ fastaq/scripts/fastaq_trim_ends
+@@ -1,7 +1,6 @@
+ #!/usr/bin/env python3
+
+ import argparse
+-from fastaq import tasks
+
+ parser = argparse.ArgumentParser(
+ description = 'Trims set number of bases off each sequence in a fasta/q file',
+@@ -11,4 +10,8 @@ parser.add_argument('start_trim', type=i
+ parser.add_argument('end_trim', type=int, help='Number of bases to trim off end')
+ parser.add_argument('outfile', help='Name of output fasta/q file')
+ options = parser.parse_args()
++
++
++from fastaq import tasks
++
+ tasks.trim(options.infile, options.outfile, options.start_trim, options.end_trim)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..dfa3826
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+delay-import-statements-for-manpage-creation.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..58f2a1b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+
+export DH_VERBOSE := 1
+export PYBUILD_NAME=fastaq
+
+mandir := $(CURDIR)/debian/man
+debfolder := $(CURDIR)/debian
+
+%:
+ dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_auto_build:
+ dh_python3
+ dh_auto_build
+ mkdir $(CURDIR)/doc
+ cd $(CURDIR)/doc
+
+override_dh_auto_clean:
+ rm -rf build .pybuild
+ rm -rf $(mandir)
+
+override_dh_installman:
+ mkdir -p $(mandir)
+ $(debfolder)/usage_to_man
+ dh_installman --
\ No newline at end of file
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..46ebe02
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
\ No newline at end of file
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/usage_to_man b/debian/usage_to_man
new file mode 100755
index 0000000..ff45c2b
--- /dev/null
+++ b/debian/usage_to_man
@@ -0,0 +1,142 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+#Converts Fastaq python scripts usage into man pages.
+#The man pages are placed in the man folder of the main Fastaq directory
+
+createManPages();
+
+sub createManPages {
+
+ my $source= 'scripts';
+ my $destination= 'debian/man';
+ my $app_name = 'Fastaq';
+ my $descriptions = shortDescription();
+
+ unless ( -d $destination ) {
+ system(mkdir $destination);
+ }
+
+ my @files;
+
+ push(@files,`ls $source/fastaq_*`);
+
+ if ( scalar @files > 0 ) {
+
+ print "Creating manpages\n";
+ for my $file ( @files ) {
+ $file =~ s/\n$//;
+
+ my $filename = $file;
+ $filename =~ s/$source\///;
+
+ my $uc_filename = uc($filename);
+ my $man_file = $filename;
+
+ $man_file = $destination . '/' . $man_file . '.1';
+
+ open (my $man_fh, ">", $man_file);
+
+ my $grep_string = $filename . ': error: too few arguments';
+
+ my $cmd = "help2man -m $filename -n $filename --no-discard-stderr $file | sed 's/usage://gi'";
+ my @output;
+ push(@output, `$cmd`);
+
+ for my $line (@output) {
+ $line =~ s/\n$//;
+
+ }
+
+ for (my $i = 0; $i < scalar @output; $i++) {
+ my $output_line = $output[$i];
+
+ if ($output_line =~ m/^\.TH/) {
+ $output_line =~ s/\s+/ /g;
+ $output_line =~ s/(\.TH) ("\d+") ("[a-zA-Z0-9_ ]*") ("[a-zA-Z0-9_<>\[\]\/\.\(\), ]*") ("[a-zA-Z0-9_]*")/$1 $uc_filename $2 $3 "$app_name" "Fastaq executables"/;
+ }
+
+ $output_line =~ s/ \\- $filename/$filename \- $descriptions->{$filename}/;
+
+ if ( $output_line =~ m/^.PP/ && $output[$i + 1] =~ m/^$filename\:/ ) {
+ $output_line = $output[$i + 1] = '';
+ }
+
+ if ($output_line =~ m/^\.SH "SEE ALSO"/) {
+ last;
+ }
+ print $man_fh "$output_line\n";
+ }
+
+ writeAuthorAndCopyright($man_fh,$filename);
+ close($man_fh);
+ }
+ print "Manpage creation complete\n";
+ }
+}
+
+sub writeAuthorAndCopyright {
+
+ my ($man_fh,$filename) = @_;
+
+ my $author_blurb = <<END_OF_AUTHOR_BLURB;
+.SH "AUTHOR"
+.sp
+$filename was originally written by Martin Hunt (mh12\@sanger.ac.uk)
+END_OF_AUTHOR_BLURB
+
+ print $man_fh "$author_blurb\n";
+
+ my $copyright_blurb = <<'END_OF_C_BLURB';
+.SH "COPYING"
+.sp
+Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&.
+END_OF_C_BLURB
+
+ print $man_fh "$copyright_blurb\n";
+
+}
+
+
+sub shortDescription {
+
+ my %descriptions = (
+ fastaq_capillary_to_pairs => 'makes an interleaved file of read pairs',
+ fastaq_chunker => 'splits a multi fasta/q file into separate files',
+ fastaq_count_sequences => 'counts the number of sequences in a fasta/q file',
+ fastaq_deinterleave => 'deinterleaves fasta/q file',
+ fastaq_enumerate_names => 'renames sequences in a file, calling them 1,2,3...',
+ fastaq_expand_nucleotides => 'makes all combinations of sequences in input file',
+ fastaq_extend_gaps => 'extends the length of all gaps in a fasta/q file',
+ fastaq_fasta_to_fastq => 'given a fasta and qual file, makes a fastq file',
+ fastaq_filter => 'filters a fasta/q file by sequence length and/or by name',
+ fastaq_get_ids => 'gets ids from each sequence in a fasta or fastq file',
+ fastaq_get_seq_flanking_gaps => 'gets the sequences either side of gaps in a fasta/q file',
+ fastaq_insert_or_delete_bases => 'deletes or inserts bases at given position(s)',
+ fastaq_interleave => 'interleaves two fasta/q files',
+ fastaq_long_read_simulate => 'simulates long reads from a fasta/q file',
+ fastaq_make_random_contigs => 'makes a multi-fasta file of random sequences',
+ fastaq_merge => 'converts multi fasta/q file to single sequence file',
+ fastaq_replace_bases => 'replaces all occurences of one letter with another',
+ fastaq_reverse_complement => 'reverse complements all sequences',
+ fastaq_scaffolds_to_contigs => 'creates a file of contigs from a file of scaffolds',
+ fastaq_search_for_seq => 'searches for an exact match on a given string and its reverese complement. guaranteed to find all hits',
+ fastaq_sequence_trim => 'trims sequences off the start of all sequences in a pair of fasta/q files',
+ fastaq_split_by_base_count => 'splits a multi fasta/q file into separate files',
+ fastaq_strip_illumina_suffix => 'strips /1 or /2 off the end of every read name',
+ fastaq_to_fake_qual => 'makes fake quality scores file',
+ fastaq_to_fasta => 'converts sequence file to fasta format',
+ fastaq_to_mira_xml => 'creates an xml file from a fasta/q file of reads, for use with mira assembler',
+ fastaq_to_orfs_gff => 'writes a gff file of open reading frames',
+ fastaq_to_perfect_reads => 'makes perfect paired end fastq reads',
+ fastaq_to_random_subset => 'takes a random subset of reads',
+ fastaq_to_tiling_bam => 'makes a bam file containing perfect (unpaired) reads tiling the whole genome',
+ fastaq_to_unique_by_id => 'removes duplicate sequences',
+ fastaq_translate => 'translates all sequences',
+ fastaq_trim_ends => 'trims set number of bases off each sequence',
+ fastaq_trim_Ns_at_end => 'trims any ns off each sequence'
+ );
+
+ return(\%descriptions);
+}
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..46c1516
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+https://github.com/sanger-pathogens/fastaq/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq_tmp.git
More information about the debian-med-commit
mailing list