debian/changelog

-mapsembler2 (2.2.4+dfsg-2) UNRELEASED; urgency=medium
+mapsembler2 (2.2.4+dfsg-2) unstable; urgency=medium
 
+  [ Steffen Moeller ]
   * Created debian/upstream/metadata
 
- -- Steffen Moeller <moeller@debian.org>  Tue, 26 Sep 2017 14:38:54 +0200
+  [ Andreas Tille ]
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * d/rules:
+     - Drop unneeded get-orig-source target
+     - Do not parse d/changelog
+  * Fix spelling
+  * Create manpages before package creation
+
+ -- Andreas Tille <tille@debian.org>  Wed, 10 Oct 2018 15:07:09 +0200
 
 mapsembler2 (2.2.4+dfsg-1) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -4,17 +4,16 @@ Uploaders: Olivier Sallou <osallou@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                cmake,
                bc,
                zlib1g-dev,
-               help2man,
                libhdf5-dev,
                libcppunit-dev,
                libboost-dev
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mapsembler2.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/mapsembler2.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/mapsembler2
+Vcs-Git: https://salsa.debian.org/med-team/mapsembler2.git
 Homepage: http://colibread.inria.fr/mapsembler2/
 
 Package: mapsembler2

debian/createmanpages

+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=mapsembler2_extremities
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="performs the first step of Mapsembler2_extend" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=mapsembler_extend
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=mapsembler2_kissreads
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="Checks for each sequence contained into the toCheck.fasta if it is read coherent with reads from readsA.fasta or readsB.fasta" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=mapsembler2_kissreads_graph
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="maps the provided reads on the graph" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=run_mapsembler2_pipeline
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="pipelines the mapsembler2 tools" \
+            --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/mans/mapsembler2_extremities.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
+.TH MAPSEMBLER2_EXTREMITIES "1" "October 2018" "mapsembler2_extremities 2.2.4" "User Commands"
+.SH NAME
+mapsembler2_extremities \- performs the first step of Mapsembler2_extend
+.SH SYNOPSIS
+.B mapsembler2_extremities
+\fB\-\-k\fR <kmersize> \fB\-\-starters\fR <fasta> \fB\-\-reads\fR <dataset> \fB\-\-output\fR <substarterfile> [optional arguments]
+.SH DESCRIPTION
+This modules performs the first step of Mapsembler2_extend. For each starter, it outputs a list of extremities of the starter (of length *k*) are found in the reads, up to 1 indel or mismatch.
+.SH OPTIONS
+.TP
+\fB\-\-k\fR (1 arg):
+kmer size that will be used for mapsembler2  [default '']
+.TP
+\fB\-\-starters\fR (1 arg):
+starters fasta file  [default '']
+.TP
+\fB\-\-reads\fR(1 arg):
+reads dataset file name. Several reads sets can be provided, surrounded by "'s and separated by a space (e.g. \fB\-\-reads\fR "reads1.fa reads2.fa")  [default '']
+.TP
+\fB\-\-output\fR (1 arg):
+output substarters file name  [default '']
+.TP
+\fB\-\-min\-solid\-subkmer\fR (1 arg):
+minimim abundance to keep a subkmer  [default '3']
+.TP
+\fB\-debug\fR (0 arg):
+debugging
+.TP
+\fB\-nb\-cores\fR (1 arg):
+number of cores  [default '0']
+.TP
+\fB\-verbose\fR (1 arg):
+verbosity level  [default '1']
+.TP
+\fB\-help\fR (0 arg):
+display help about possible options
+.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/mapsembler2_kissreads.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
+.TH MAPSEMBLER2_KISSREADS "1" "October 2018" "mapsembler2_kissreads 2.2.4" "User Commands"
+.SH NAME
+mapsembler2_kissreads \- Checks for each sequence contained into the toCheck.fasta if it is read coherent with reads from readsA.fasta or readsB.fasta
+.SH SYNOPSIS
+.B mapsembler2_kissreads
+<toCheck.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-k value] [\-c value] [\-d value] [\-O value] [\-o name] [\-u name] [\-n] [\-I] [\-i index_stride] [\-m align_file] [\-s] [\-f] [\-h]
+.SH DESCRIPTION
+Checks for each sequence contained into the toCheck.fasta if
+it is read coherent (each position is covered by at least "min_coverage" read(s)) with reads from readsA.fasta or readsB.fasta
+A sequence s from toCheck is treated as follow:
+.IP
+if (s coherent with at least one read set): output the sequence as follows
+.IP
+>original fasta comment|C1:min<avg\-corr_avg<max|C2:min<avg\-cor_avg<max|C3...:
+>s
+.IP
+With A:min<avg\-cor_avg<max standing for : value of the position having minimal coverage in readsA.fasta < average coverage in readsA.fasta \- R\-squarred corrected average in readsA.fa < value of the position having maximal coverage in readsA.fasta
+The coverage is the number of reads that perfectly mapped a position
+Any other situation (s not coherent with any): couple non read coherent, not outputed
+.SH OPTIONS
+.HP
+\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 25.
+.HP
+\fB\-O\fR minimal_read_overlap: a read can be mapped if its overlap is a least "minimal_read_overlap". Default: k
+.HP
+\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2
+.HP
+\fB\-d\fR max_substitutions: Maximal number of substitutions authorized between a read and a fragment. Note that no substitution is allowed on the central position while anaylizing the kissnp output. Default: 1.
+.HP
+\fB\-o\fR file_name: write read\-coherent outputs. Default: standard output
+.HP
+\fB\-u\fR file_name: write unread\-coherent outputs. Default: standard output
+.HP
+\fB\-n\fR the input file (toCheck.fasta) is a kissnp output (incompatible with \fB\-I\fR option)
+.IP
+in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.
+.HP
+\fB\-I\fR the input file (toCheck.fasta) is an Intl output (incompatible with \fB\-n\fR option)
+.HP
+\fB\-i\fR index_stride (int value). This is a heuristic for limiting the memory footprint. Instead of indexing each kmer of the sequences contained into the toCheck.fasta, kissreads indexes kmers occurring each "index_stride" position. Default = 1 (no heuristic)
+.HP
+\fB\-t\fR max number of threads (also limited by number of input files)
+.HP
+\fB\-m\fR align_file, write a file of reads mapped to sequences in file align_file
+.HP
+\fB\-s\fR silent mode
+.HP
+\fB\-f\fR outputs coherent events in a standard fasta file format
+.HP
+\fB\-h\fR prints this message and exit
+.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/mapsembler2_kissreads_graph.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
+.TH MAPSEMBLER2_KISSREADS_GRAPH "1" "October 2018" "mapsembler2_kissreads_graph 2.2.4" "User Commands"
+.SH NAME
+mapsembler2_kissreads_graph \- maps the provided reads on the graph
+.SH SYNOPSIS
+.B mapsembler2_kissreads_graph
+input_graph <readsC1.fasta/fastq[.gz]> [<readsC2.fasta/fastq[.gz]> [<readsC3.fasta/fastq[.gz] ...] \fB\-M\fR \fB\-t\fR type [\-k value] [\-c min_coverage] [\-d max_substitutions] [\-o name] [\-h]
+.SH DESCRIPTION
+mapsembler2_kissreads_graph maps the provided reads on the graph
+With option "\-t coverage": outputs an equivalent graph removing uncovered edges and adding:
+.IP
+for each node: the coverage per sample and per position
+.IP
+for each edge: the number of mapped reads per sample using this edge
+.P
+With option "-t modify": outputs the same simplified graph:
+.IP
+removing low covered edges and nodes (less that min_coverage)
+then phasing simple non branching paths
+.PP
+If \fB\-M\fR option is specified, the input is considered as a Mapsembler output \- thus composed of multiple independent graphes
+.SH OPTIONS
+.SS MANDATORY
+.HP
+\fB\-t\fR <type>
+.IP
+"c" "coverage"
+.IP
+"m" "modify"
+.SS OPTIONAL
+\fB\-M\fR: the input is considered as a Mapsembler output
+.HP
+\fB\-o\fR file_name: write obtained graph. Default: standard output
+.HP
+\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 25.
+.HP
+\fB\-c\fR min_coverage: Will consider an edge as coherent if coverage (number of reads from all sets using this edge) is at least min_coverage. Default: 2
+.HP
+\fB\-d\fR max_substitutions: Will map a read on the graph with at most max_substitutions substitutions. Default: 1
+.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/mapsembler_extend.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
+.TH MAPSEMBLER_EXTEND "1" "October 2018" "mapsembler_extend 2.2.4" "User Commands"
+.SH NAME
+mapsembler_extend \- extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly
+.SH SYNOPSIS
+.B mapsembler_extend
+<extrem_kmers.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-t extension_type] [\-k value] [\-c value] [\-g value] [\-i index_name] [\-o name] [\-h]
+.SH DESCRIPTION
+Mapsembler 2 extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly.
+.SH OPTIONS
+.HP
+\fB\-t\fR extension_type. Default: 1
+.IP
+1: a strict sequence: any branching stops the extension
+.IP
+2: a consensus sequence: contiging approach
+.IP
+3: a strict graph: any branching is conserved in the graph
+.IP
+4: a consensus graph: "small" polymorphism is merged, but "large" structures are represented
+.HP
+\fB\-k\fR size_kmers: Size of the k\-mers used duriung the extension phase Default: 31. Accepted range, depends on the compilation (make k=42 for instance)
+.HP
+\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2
+.HP
+\fB\-g\fR estimated_genome_size: estimation of the size of the genome whose reads come from.
+.IP
+It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion
+.HP
+\fB\-x\fR node_len: limit max of nodes length. Default: 40
+.HP
+\fB\-y\fR graph_max_depth: limit max of graph depth.Default: 10000
+.HP
+\fB\-i\fR index_name: stores the index files in files starting with this prefix name. Can be re\-used latter. Default: "index"
+.IP
+IF THE FILE "index_name.bloom" EXISTS: the index is not re\-created
+.HP
+\fB\-o\fR file_name_prefix: where to write outputs. Default: "res_mapsembler"
+.HP
+\fB\-p\fR search_mod: kind of prosses Breadth or Depth. Default: Breadth
+.HP
+\fB\-h\fR prints this message and exit
+.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/run_mapsembler2_pipeline.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
+.TH RUN_MAPSEMBLER2_PIPELINE "1" "October 2018" "run_mapsembler2_pipeline 2.2.4" "User Commands"
+.SH NAME
+run_mapsembler2_pipeline \- pipelines the mapsembler2 tools
+.SH SYNOPSIS
+.B run_mapsembler_and_phaser.sh
+\fI\,-s <starter.fasta> -r <reads.faste> -t \/\fR[\fI\,1/2/3/4\/\fR]\fI\,<options>\/\fR
+.SH DESCRIPTION
+run_mapsembler_pipeline.sh, a pipelining mapsembler2_extremities, mapsembler2_extend and kissread_g
+.SH OPTIONS
+.HP
+\fB\-s\fR: file containing starters (fasta)
+.HP
+\fB\-r\fR list of reads separated by space, surrounded by the '"' character. Note that reads may be in fasta or fastq format, gzipped or not. Example: \fB\-r\fR "data_sample/reads_sequence1.fasta   data_sample/reads_sequence2.fasta.gz".
+.HP
+\fB\-t\fR: kind of assembly: 1=unitig (fasta), 2=contig (fasta), 3=unitig (graph), 4=contig(graph)
+.SS OPTIONAL
+.HP
+\fB\-p\fR prefix. All out files will start with this prefix. Example: \fB\-p\fR my_prefix
+.HP
+\fB\-k\fR value. Set the length of used kmers. Must fit the compiled value. Default=31. Example \fB\-k\fR 31
+.HP
+\fB\-c\fR value. Set the minimal coverage. Default=5. Example \fB\-c\fR 5
+.HP
+\fB\-d\fR value. Set the number of authorized substitutions used while mapping reads on found SNPs. Default=1. Example: \fB\-d\fR 1
+.HP
+\fB\-g\fR value. Estimated genome size. Used only to control memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM. Default=10 million. Example: \fB\-d\fR 10000000
+.HP
+\fB\-f\fR value. Set the process of search in the graph (1=Breadth  and 2=Depth). Default=1. Example: \fB\-f\fR 1
+.HP
+\fB\-x\fR value. Set the maximal nodes length . Default=40. Example: \fB\-x\fR 40
+.HP
+\fB\-y\fR value. Set the maximal graph depth . Default=10000. Example: \fB\-y\fR 10000
+.HP
+\fB\-h\fR Prints this message and exist
+.SH SEE ALSO
+Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr
+.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/mapsembler2.manpages

-mapsembler2_extremities.1
-mapsembler_extend.1
-mapsembler2_kissreads.1
-mapsembler2_kissreads_graph.1
-run_mapsembler2_pipeline.1
-
+debian/mans/*.1

debian/patches/fix_build

-Subject: Add hardening
-Description: makefiles do not import default CFLAGS,...
-this patch add debian cflags for hardening
-Forwarded: no
-Author: Olivier Sallou <osallou@debian.org>
-Last-Updated: 2014-02-01
---- a/minia/makefile
-+++ b/minia/makefile
-@@ -1,5 +1,9 @@
- CC=g++
--CFLAGS = -O4
-+
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-+
- SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
- EXEC=minia
- OBJ= $(SRC:.cpp=.o)
-@@ -60,7 +64,7 @@
- all: $(EXEC)
- 
- minia: clean $(OBJ) Minia.cpp
--	$(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
-+	$(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz
- 
- %.o: %.cpp %.h
- 	$(CC) -o $@ -c $< $(CFLAGS)
---- a/maps/makefile
-+++ b/maps/makefile
-@@ -1,7 +1,10 @@
- CC=g++ 
- EXEC=mapsembler
- #CFLAGS=  -O4 -lz --std=gnu++0x
--CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -g -lz -DMINIA_IS_IN_PARENT_FOLDER
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-+
- #CFLAGS=  -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
- #CFLAGS=  -g -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER
- #CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER
-@@ -49,7 +52,7 @@
- 
- mapsembler:  $(OBJ) $(OBJ2) mapsembler.cpp
- #mapsembler:  $(OBJ) $(OBJ2) test.cpp
--	$(CC) -o $@ $^ $(CFLAGS) 
-+	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
- 
- %.o: %.cpp %.h 
- 	$(CC) -lz -o $@ -c $< $(CFLAGS)
---- a/kissreads_g/makefile
-+++ b/kissreads_g/makefile
-@@ -4,7 +4,9 @@
- #Loader.cpp CFLAGS=  -g -lz -std=c++11 -DMINIA_IS_IN_PARENT_FOLDER
- #Loader.cpp 
- #CFLAGS=  -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
--CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -g -lz -DMINIA_IS_IN_PARENT_FOLDER
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
- SRC=block_allocator.cpp  DeBruijnGraph.cpp  Fragment.cpp  json.cpp  read_coherence_mapsembler/libchash.cpp     read_coherence_mapsembler/couple.cpp  read_coherence_mapsembler/misc_tools.cpp  read_coherence_mapsembler/read_groups.cpp read_coherence_mapsembler/consensus_common.cpp  read_coherence_mapsembler/list.cpp    read_coherence_mapsembler/read_coherence.cpp  read_coherence_mapsembler/interface_libchash.cpp commons.cpp ../minia/Kmer.cpp ../minia/Bank.cpp Loader.cpp BooleanVector.cpp ReadMapper.cpp
- OBJ= $(SRC:.cpp=.o) 
- all: $(EXEC)
-@@ -48,7 +50,7 @@
- all: $(EXEC)
- 
- kissreads_graph:  $(OBJ) KissReadsGraph.cpp
--	$(CC) -o $@ $^ $(CFLAGS)
-+	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
- 
- %.o: %.cpp %.h
- 	$(CC) -lz -o $@ -c $< $(CFLAGS)

debian/patches/fix_makefile

-Subject: Add hardening
-Description: makefiles do not import default CFLAGS,...
-this patch add debian cflags for hardening
-Forwarded: no
-Author: Olivier Sallou <osallou@debian.org>
-Last-Updated: 2014-02-21
---- a/maps/makefile
-+++ b/maps/makefile
-@@ -49,11 +49,16 @@
- 
- mapsembler:  $(OBJ) $(OBJ2) mapsembler.cpp
- #mapsembler:  $(OBJ) $(OBJ2) test.cpp
--	$(CC) -o $@ $^ $(CFLAGS) 
-+	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
- 
- %.o: %.cpp %.h 
- 	$(CC) -lz -o $@ -c $< $(CFLAGS)
- 
-+CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
-+LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
-+
-+
- 
- #%.o: %.c %.h 
- #	$(CC) -o $@ -c $< $(CFLAGS)

debian/patches/fix_path

-Subject: use Debian paths
-Description: update some paths to use Debian package paths
-Last-Updated: 2014-02-01
-Author: Olivier Sallou <osallou@debian.org>
-Forwarded: no
---- a/run_mapsembler_and_phaser.sh
-+++ b/run_mapsembler_and_phaser.sh
-@@ -1,8 +1,9 @@
-+#!/bin/bash
- #######################################################################
- #################### HEADER, CHANGE VALUES HERE #######################
- #######################################################################
--starters_file="sample_example/fragments.fa"
--read_sets="sample_example/reads.fa" # FOR instance: "read_set1.fa.gz read_set2.fq.gz"
-+starters_file="/usr/share/doc/mapsembler2/sample_example/fragments.fa"
-+read_sets="/usr/share/doc/mapsembler2/sample_example/reads.fa.gz" # FOR instance: "read_set1.fa.gz read_set2.fq.gz"
- prefix_index="index" # all files used for indexing will be written will start with this prefix
- prefix_results="res" # all final files will be written will start with this prefix
- k=31 # size of kmers
-@@ -10,7 +11,7 @@
- d=1 # estimated number of error per read (used by kissreads only)
- g=10000000 # estimated genome size. Used only to control kissnp2 memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM.
- t=0
--PATH_TOOLS="./tools/" # path were executables kissnp2 and kissreads are. Leave blank if they are located in a directory located in the PATH environnement variable
-+PATH_TOOLS="/usr/bin/" # path were executables kissnp2 and kissreads are. Leave blank if they are located in a directory located in the PATH environnement variable
- #######################################################################
- #################### END HEADER                 #######################
- #######################################################################

debian/patches/series

@@ -4,3 +4,4 @@ add_hardening
 skip_mphe
 gcc-5.patch
 libgomp.patch
+spelling.patch

debian/patches/spelling.patch

+Description: Fix spelling
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 10 Oct 2018 12:49:34 +0200
+
+--- a/kissreads_graph/KissReadsGraph.cpp
++++ b/kissreads_graph/KissReadsGraph.cpp
+@@ -35,7 +35,7 @@ void print_usage_and_exit(char * name){
+ 	fprintf (stderr, "With option \"-t modify\": outputs the same simplified graph:\n");
+ 	fprintf (stderr, "\t removing low covered edges and nodes (less that min_coverage)\n");
+     fprintf (stderr, "\t then phasing simple non branching paths\n");
+-    fprintf (stderr, "If -M option is specified, the input is considered as a Mapsembler output - thus composed of multiple independant graphes\n");
++    fprintf (stderr, "If -M option is specified, the input is considered as a Mapsembler output - thus composed of multiple independent graphes\n");
+     
+     
+ 	fprintf (stderr, "\nMANDATORY\n");
+--- a/mapsembler2_extend/IterativeExtensions.cpp
++++ b/mapsembler2_extend/IterativeExtensions.cpp
+@@ -178,7 +178,7 @@ void IterativeExtensions::construct_line
+             revcomp_sequence(kmer_seq,sizeKmer);
+ 
+         if (debug)
+-            printf(" --- iteration: kmer %s%s (of lenght %d) depth %d nbNodes explored %lli ---\n",kmer_seq,strand?" (internally rc)":"", (int)strlen(kmer_seq), depth,nbNodes);
++            printf(" --- iteration: kmer %s%s (of length %d) depth %d nbNodes explored %lli ---\n",kmer_seq,strand?" (internally rc)":"", (int)strlen(kmer_seq), depth,nbNodes);
+ 
+         // right extension
+         int len_right = traversal->traverse(kmer,right_traversal,strand);
+@@ -397,7 +397,7 @@ void IterativeExtensions::construct_line
+             revcomp_sequence(kmer_seq,sizeKmer);
+         
+         if (debug)
+-            printf("iteration: kmer %s%s (of lenght %zu) depth %d nbNodes explored %lli\n",kmer_seq,strand?" (internally rc)":"", strlen(kmer_seq), depth,nbNodes);
++            printf("iteration: kmer %s%s (of length %zu) depth %d nbNodes explored %lli\n",kmer_seq,strand?" (internally rc)":"", strlen(kmer_seq), depth,nbNodes);
+         
+         // right extension
+         int len_right = traversal->traverse(kmer,right_traversal,strand);

debian/rules

@@ -7,7 +7,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
 
-SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
+include /usr/share/dpkg/default.mk
 
 ifneq ($(wildcard /usr/include/hdf5/serial),)
   export DEB_CPPFLAGS_MAINT_APPEND := -I/usr/include/hdf5/serial
@@ -22,9 +22,6 @@ LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
 %:
 	dh $@
 
-get-orig-source:
-	uscan --verbose --force-download
-
 override_dh_auto_build:
 	mkdir mapsembler2_extremities/build
 	cd mapsembler2_extremities/build && cmake .. && make
@@ -42,20 +39,10 @@ override_dh_clean:
 	cd kissreads && make clean
 	rm -f kissreads/mapsembler2_kissreads
 
-	rm -f mapsembler2_extremities.1
-	rm -f mapsembler_extend.1
-	rm -f kissreads.1
-	rm -f kissreads_graph.1
 	dh_clean
 
 override_dh_install:
-	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extremities/build/mapsembler2_extremities > mapsembler2_extremities.1
-	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend > mapsembler_extend.1
 	mv ./kissreads/kissreads ./kissreads/mapsembler2_kissreads
-	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads/mapsembler2_kissreads > mapsembler2_kissreads.1
 	mv ./kissreads_graph/kissreads_graph ./kissreads_graph/mapsembler2_kissreads_graph
-	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads_graph/mapsembler2_kissreads_graph > mapsembler2_kissreads_graph.1
 	cp run_mapsembler2_pipeline.sh run_mapsembler2_pipeline
-	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./run_mapsembler2_pipeline > run_mapsembler2_pipeline.1
 	dh_install
-