debian/copyright

@@ -10,7 +10,7 @@ Copyright: 2014-2018 Genscale research team
                      Erwan Drezen and Guillaume Rizk and Rayan Chikhi and
                      Charles Deltel and Claire Lemaitre and
                      Pierre Peterlongo and Dominique Lavenier
-License: GPL-Affero-3
+License: GNU-Affero-3
 
 Files: gatb-core/thirdparty/json/json.hpp
 Copyright: 2014-2016 Neil
@@ -18,12 +18,35 @@ License: DWTFYWPL
  Do what the fuck you want public license.
 Comment: Downloaded from https://github.com/nbsdx/SimpleJSON/blob/master/json.hpp
 
+Files: gatb-core/src/gatb/bcalm2/ThreadPool.h
+Copyright: 2012 Jakob Progsch, Václav Zeman
+License: zlib
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+ .
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+ .
+   1. The origin of this software must not be misrepresented; you must not
+   claim that you wrote the original software. If you use this software
+   in a product, an acknowledgment in the product documentation would be
+   appreciated but is not required.
+ .
+   2. Altered source versions must be plainly marked as such, and must not be
+   misrepresented as being the original software.
+ .
+   3. This notice may not be removed or altered from any source
+   distribution.
+Comment: Downloaded from https://github.com/progschj/ThreadPool
+
 Files: debian/*
 Copyright: 2017 Nadiya Sitdykova <rovenskasa@gmail.com>
            2018 Andreas Tille <tille@debian.org>
-License: GPL-Affero-3
+License: GNU-Affero-3
 
-License: GPL-Affero-3
+License: GNU-Affero-3
        Preamble
  .
  The GNU Affero General Public License is a free, copyleft license for

debian/createmanpages

+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=leon
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='reference free compression for NGS reads' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=dbginfo
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='dumps information about a DeBruinj graph build by dbgh5' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=dbgh5
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='builds a DeBruijn graph from a set of reads and save it as a HDF5 file' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+

debian/manpages

+debian/mans/*.1

debian/mans/dbgh5.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH DBGH5 "1" "May 2018" "dbgh5 1.4.1" "User Commands"
+.SH NAME
+dbgh5 \- builds a DeBruijn graph from a set of reads and save it as a HDF5 file
+.SH DESCRIPTION
+gatb\-core\-library
+.TP
+version
+: 1.4.1
+.TP
+build_kmer_size
+: 32 64 96 128
+.PP
+[graph options]
+.TP
+\fB\-no\-mphf\fR
+(0 arg) :    don't construct the MPHF
+.IP
+[kmer count options]
+.TP
+\fB\-in\fR
+(1 arg) :    reads file
+.TP
+\fB\-kmer\-size\fR
+(1 arg) :    size of a kmer  [default '31']
+.TP
+\fB\-abundance\-min\fR
+(1 arg) :    min abundance threshold for solid kmers  [default '2']
+.TP
+\fB\-abundance\-max\fR
+(1 arg) :    max abundance threshold for solid kmers  [default '2147483647']
+.TP
+\fB\-abundance\-min\-threshold\fR
+(1 arg) :    min abundance hard threshold (only used when min abundance is "auto")  [default '2']
+.TP
+\fB\-histo\-max\fR
+(1 arg) :    max number of values in kmers histogram  [default '10000']
+.TP
+\fB\-solidity\-kind\fR
+(1 arg) :    way to compute counts of several files (sum, min, max, one, all, custom)  [default 'sum']
+.TP
+\fB\-solidity\-custom\fR
+(1 arg) :    when solidity\-kind is cutom, specifies list of files where kmer must be present  [default '']
+.TP
+\fB\-max\-memory\fR
+(1 arg) :    max memory (in MBytes)  [default '5000']
+.TP
+\fB\-max\-disk\fR
+(1 arg) :    max disk   (in MBytes)  [default '0']
+.TP
+\fB\-solid\-kmers\-out\fR
+(1 arg) :    output file for solid kmers (only when constructing a graph)  [default '']
+.TP
+\fB\-out\fR
+(1 arg) :    output file  [default '']
+.TP
+\fB\-out\-dir\fR
+(1 arg) :    output directory  [default '.']
+.TP
+\fB\-out\-tmp\fR
+(1 arg) :    output directory for temporary files  [default '.']
+.TP
+\fB\-out\-compress\fR
+(1 arg) :    h5 compression level (0:none, 9:best)  [default '0']
+.TP
+\fB\-storage\-type\fR
+(1 arg) :    storage type of kmer counts ('hdf5' or 'file')  [default 'hdf5']
+.IP
+[kmer count, algorithmic options options]
+.TP
+\fB\-minimizer\-type\fR
+(1 arg) :    minimizer type (0=lexi, 1=freq)  [default '0']
+.TP
+\fB\-minimizer\-size\fR
+(1 arg) :    size of a minimizer  [default '10']
+.TP
+\fB\-repartition\-type\fR (1 arg) :
+minimizer repartition (0=unordered, 1=ordered)  [default '0']
+.IP
+[bloom options]
+.TP
+\fB\-bloom\fR
+(1 arg) :    bloom type ('basic', 'cache', 'neighbor')  [default 'neighbor']
+.TP
+\fB\-debloom\fR
+(1 arg) :    debloom type ('none', 'original' or 'cascading')  [default 'cascading']
+.TP
+\fB\-debloom\-impl\fR (1 arg) :
+debloom impl ('basic', 'minimizer')  [default 'minimizer']
+.IP
+[branching options]
+.TP
+\fB\-branching\-nodes\fR (1 arg) :
+branching type ('none' or 'stored')  [default 'stored']
+.TP
+\fB\-topology\-stats\fR
+(1 arg) :    topological information level (0 for none)  [default '0']
+.IP
+[general options]
+.TP
+\fB\-config\-only\fR
+(0 arg) :    dump config only
+.TP
+\fB\-nb\-cores\fR
+(1 arg) :    number of cores  [default '0']
+.TP
+\fB\-verbose\fR
+(1 arg) :    verbosity level  [default '1']
+.TP
+\fB\-integer\-precision\fR (1 arg) :
+integers precision (0 for optimized value)  [default '0']
+.TP
+\fB\-email\fR
+(1 arg) :    send statistics to the given email address  [default '']
+.TP
+\fB\-email\-fmt\fR
+(1 arg) :    'raw' or 'xml'  [default 'raw']
+.TP
+\fB\-check\fR
+(1 arg) :    check result with previous result  [default '']
+.TP
+\fB\-check\-dump\fR
+(1 arg) :    dump some properties of the created graph into a file  [default '']
+.TP
+[debug
+options]
+.TP
+\fB\-redo\-bcalm\fR (0 arg) :
+debug function, redo the bcalm algo
+.TP
+\fB\-skip\-bcalm\fR (0 arg) :
+same, but       skip     bcalm
+.TP
+\fB\-redo\-bglue\fR (0 arg) :
+same, but       redo     bglue
+.TP
+\fB\-skip\-bglue\fR (0 arg) :
+same, but       skip     bglue
+.TP
+\fB\-redo\-links\fR (0 arg) :
+same, but       redo     links
+.TP
+\fB\-skip\-links\fR (0 arg) :
+same, but       skip     links
+.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/mans/dbginfo.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH DBGINFO "1" "May 2018" "dbginfo 1.4.1" "User Commands"
+.SH NAME
+dbginfo \- dumps information about a DeBruinj graph build by dbgh5
+.SH OPTIONS
+.TP
+\fB\-in\fR (1 arg) :
+graph file
+.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/mans/leon.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH LEON "1" "May 2018" "leon 1.4.1" "User Commands"
+.SH NAME
+leon \- reference free compression for NGS reads
+.SH OPTIONS
+.SS leon options
+.TP
+\fB\-file\fR
+(1 arg) :    input file (e.g. FASTA/FASTQ for compress or .leon file for decompress)
+.TP
+\fB\-c\fR
+(0 arg) :    compression
+.TP
+\fB\-d\fR
+(0 arg) :    decompression
+.TP
+\fB\-nb\-cores\fR
+(1 arg) :    number of cores (default is the available number of cores)  [default '0']
+.TP
+\fB\-lossless\fR
+(0 arg) :    switch to lossless compression for qualities (default is lossy. lossy has much higher compression rate, and the loss is in fact a gain. lossy is better!)
+.SS compression options
+.TP
+\fB\-kmer\-size\fR
+(1 arg) :    size of a kmer  [default '31']
+.TP
+\fB\-abundance\fR
+(1 arg) :    abundance threshold for solid kmers (default inferred)  [default '']
+.TP
+\fB\-init\-iterator\fR
+(0 arg) :    init iterator for ibank mode
+.TP
+\fB\-seq\-only\fR
+(0 arg) :    store dna seq only, header and quals are discarded, will decompress to fasta (same as \fB\-noheader\fR \fB\-noqual\fR)
+.TP
+\fB\-noheader\fR
+(0 arg) :    discard header
+.TP
+\fB\-noqual\fR
+(0 arg) :    discard quality scores
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.