...
 
Commits (12)
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
......
......@@ -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
......
#!/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
.\" 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.
.\" 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.
.\" 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.
.\" 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.
.\" 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.
mapsembler2_extremities.1
mapsembler_extend.1
mapsembler2_kissreads.1
mapsembler2_kissreads_graph.1
run_mapsembler2_pipeline.1
debian/mans/*.1
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)
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)
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 #######################
#######################################################################
......@@ -4,3 +4,4 @@ add_hardening
skip_mphe
gcc-5.patch
libgomp.patch
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);
......@@ -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