bio-velvet_underground 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: fb4a2dda523583497755b908d85e6b5688562582
+  data.tar.gz: 24da3eeb3f3f25818527db4ed3b2278d6c8e9bd8
+SHA512:
+  metadata.gz: 306e0ee16f7bef2742c1b6717d342a84e8d603240c0b217c7fde8703be30e86526ded8e4d48e0284415eebea15b5500f90351ea0e7125f201aa8567b4300feee
+  data.tar.gz: 5333a971fd4b52803aabb3fefd49658807cd790858a524f245d87d51897274853d3880c1aa33597ee6c975bcf1755a23f457667d0a963c68a725e840dfe0e747

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "ext/src"]
+	path = ext/src
+	url = https://github.com/wwood/velvet

data/.travis.yml

@@ -0,0 +1,13 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,19 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+gem 'ffi', '~> 1.9'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "pry", ">0"
+  gem "rspec", "~> 2.8"
+  gem "shoulda", ">= 0"
+  gem "yard", "~> 0.7"
+  gem "simplecov", ">= 0"
+  gem "jeweler", "~> 2.0"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+end

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2014 Ben Woodcroft
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,53 @@
+# bio-velvet_underground
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-velvet_underground.png)](http://travis-ci.org/wwood/bioruby-velvet_underground)
+
+This biogem is aimed at providing Ruby bindings to the velvet assembler's source code.
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-velvet_underground
+```
+
+## Usage
+
+The only thing implemented at this stage is access to the binary sequence file created when velveth is run with the `-create_binary` flag.
+
+```ruby
+require 'bio-velvet_underground'
+
+seqs = Bio::Velvet::Underground::BinarySequenceStore.new '/path/to/velvet/directory/CnyUnifiedSeq'
+seqs[1] #=> 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGA'
+seqs.length #=> 77 (there is 77 sequences in the CnyUnifiedSeq)
+
+```
+
+Patches to other parts of velvet welcome.
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-velvet_underground
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+This software is currently unpublished.
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-velvet_underground)
+
+## Copyright
+
+Copyright (c) 2014 Ben Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

@@ -0,0 +1,51 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-velvet_underground"
+  gem.homepage = "http://github.com/wwood/bioruby-velvet_underground"
+  gem.license = "GPL"
+  gem.summary = %Q{Bindings to some internals of the velvet assembler}
+  gem.description = %Q{Bindings to some internals of the velvet assembler.}
+  gem.email = "donttrustben@gmail.com"
+  gem.authors = ["Ben Woodcroft"]
+  # dependencies defined in Gemfile
+  gem.extensions = "ext/mkrf_conf.rb"
+
+  # by default, velvet as a git submodule is not included when making the gem
+  # but we need it to be.
+  gem.files.include "ext/src/src/*"
+  gem.files.include "ext/src/Makefile"
+  gem.files.include "ext/src/License"
+  gem.files.include "ext/src/third-party/**/*"
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :spec
+
+require 'yard'
+YARD::Rake::YardocTask.new

data/VERSION

@@ -0,0 +1 @@
+0.0.1

data/ext/bioruby.patch

@@ -0,0 +1,60 @@
+diff --git a/Makefile b/Makefile
+index 8239e72..e0308db 100644
+--- a/Makefile
++++ b/Makefile
+@@ -38,16 +38,17 @@ endif
+ 
+ OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o
+ OBJDBG = $(subst obj,obj/dbg,$(OBJ))
++OBJSHARED = $(subst obj,obj/shared,$(OBJ))
+ 
+ default : cleanobj zlib obj velveth velvetg doc
+ 
+ clean : clean-zlib
+-	-rm obj/*.o obj/dbg/*.o ./velvet* 
++	-rm obj/*.o obj/dbg/*.o obj/shared/*.o obj/shared/velvet.so.0.0.1 ./velvet* 
+ 	-rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
+ 	-rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log
+ 
+ cleanobj: 
+-	-rm obj/*.o obj/dbg/*.o 
++	-rm obj/*.o obj/dbg/*.o obj/shared/*.o
+ 
+ ifdef BUNDLEDZLIB
+ Z_LIB_DIR=third-party/zlib-1.2.3
+@@ -118,3 +119,15 @@ Manual.pdf: doc/manual_src/Manual.tex doc/manual_src/Columbus_manual.tex
+ 
+ test: velvetg velveth
+ 	cd tests && ./run-tests.sh
++
++sharedobjdir:
++	mkdir -p obj/shared
++
++obj/shared: sharedobjdir $(OBJSHARED)
++
++obj/shared/%.o: src/%.c
++	$(CC) -fPIC $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
++
++shared: zlib obj/shared
++	cd obj/shared && gcc -shared -Wl,-soname,libvelvet.so.1 -o libvelvet.so.1.0 allocArray.o autoOpen.o binarySequences.o concatenatedGraph.o concatenatedPreGraph.o correctedGraph.o dfibHeap.o dfib.o fibHeap.o fib.o graph.o graphReConstruction.o graphStats.o kmer.o kmerOccurenceTable.o locallyCorrectedGraph.o passageMarker.o preGraphConstruction.o preGraph.o readCoherentGraph.o readSet.o recycleBin.o roadMap.o scaffold.o shortReadPairs.o splay.o splayTable.o tightString.o utility.o
++
+diff --git a/src/utility.c b/src/utility.c
+index d402629..126b386 100644
+--- a/src/utility.c
++++ b/src/utility.c
+@@ -97,6 +97,7 @@ void exitErrorf(int exitStatus, boolean showErrno, const char *format, ...)
+ 
+ void velvetLog(const char *format, ...)
+ {
++/*
+   static boolean timeIsSet = false;
+   static struct timeval tvStart;
+   struct timeval tvNow;
+@@ -120,6 +121,7 @@ void velvetLog(const char *format, ...)
+ #ifdef DEBUG 
+   fflush(stdout);
+ #endif
++*/
+ }
+ 
+ void velvetFprintf(FILE * file, const char * format, ...) 

data/ext/mkrf_conf.rb

@@ -0,0 +1,50 @@
+#(c) Copyright 2011 Raoul Bonnal. All Rights Reserved. Modified by Ben Woodcroft, 2014
+
+# create Rakefile for shared library compilation
+
+
+
+path = File.expand_path(File.dirname(__FILE__))
+
+path_external = File.join(path, "../lib/bio-velvet_underground/external")
+
+version = File.open(File.join(path_external,"VERSION"),'r')
+Version = version.read
+version.close
+
+File.open(File.join(path,"Rakefile"),"w") do |rakefile|
+rakefile.write <<-RAKE
+require 'rbconfig'
+require 'fileutils'
+include FileUtils::Verbose
+require 'rake/clean'
+
+path = File.expand_path(File.dirname(__FILE__))
+path_external = File.join(File.dirname(__FILE__), "../lib/bio-velvet_underground/external")
+
+task :compile do
+  cd(File.join(File.dirname(__FILE__),'src')) do
+    sh "patch -p1 < ../bioruby.patch"
+    case Config::CONFIG['host_os']
+      when /linux/
+      sh "make shared"
+      cp("obj/shared/libvelvet.so.1.0",path_external)
+      when /darwin/
+      raise NotImplementedError, "possibly will work, but bio-velvet_underground is not tested on OSX"
+      when /mswin|mingw/ then raise NotImplementedError, "bio-velvet_underground library is not available for Windows platform"
+    end #case
+  end #cd
+end
+
+task :clean do
+  cd(File.join(path,'src')) do
+    sh "make clean"
+  end
+  rm(File.join(path_external,"libvelvet.so.1.0"))
+end
+
+task :default => [:compile]
+
+RAKE
+
+end

data/ext/src/Makefile

@@ -0,0 +1,125 @@
+CC = gcc
+CFLAGS = -Wall
+DEBUG = -g
+LIBS = -lm
+OPT = -O3
+MAXKMERLENGTH=31
+CATEGORIES=2
+DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+PDFLATEX_VERSION := $(shell pdflatex --version 2> /dev/null)
+
+# Mac OS users: uncomment the following lines
+CFLAGS = -Wall -m64
+
+# Sparc/Solaris users: uncomment the following line
+# CFLAGS = -Wall -m64
+
+ifdef BIGASSEMBLY
+override DEF := $(DEF) -D BIGASSEMBLY
+endif
+
+ifdef VBIGASSEMBLY
+override DEF := $(DEF) -D BIGASSEMBLY -D VBIGASSEMBLY
+endif 	
+
+
+ifdef LONGSEQUENCES
+override DEF := $(DEF) -D LONGSEQUENCES
+endif
+
+# OpenMP 
+ifdef OPENMP
+override CFLAGS := $(CFLAGS) -fopenmp
+endif
+
+# Per library coverage
+ifdef SINGLE_COV_CAT
+override DEF := $(DEF) -D SINGLE_COV_CAT
+endif
+
+OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o
+OBJDBG = $(subst obj,obj/dbg,$(OBJ))
+
+default : cleanobj zlib obj velveth velvetg doc
+
+clean : clean-zlib
+	-rm obj/*.o obj/dbg/*.o ./velvet* 
+	-rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
+	-rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log
+
+cleanobj: 
+	-rm obj/*.o obj/dbg/*.o 
+
+ifdef BUNDLEDZLIB
+Z_LIB_DIR=third-party/zlib-1.2.3
+Z_LIB_FILES=$(Z_LIB_DIR)/*.o
+override DEF := $(DEF) -D BUNDLEDZLIB
+
+zlib: 
+	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
+
+clean-zlib :
+	cd $(Z_LIB_DIR) && make clean
+else
+Z_LIB_FILES=-lz
+
+zlib :
+clean-zlib :
+endif
+
+velveth : obj 
+	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+
+velvetg : obj
+	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+debug : override DEF := $(DEF) -D DEBUG 
+debug : cleanobj obj/dbg
+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+color : override DEF := $(DEF) -D COLOR
+color : cleanobj obj_de
+	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
+colordebug : cleanobj obj/dbg_de
+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+objdir:
+	mkdir -p obj
+
+obj: zlib cleanobj objdir $(OBJ)
+
+obj_de: override DEF := $(DEF) -D COLOR
+obj_de: zlib cleanobj objdir $(OBJ)
+
+obj/dbgdir: 
+	mkdir -p obj/dbg
+
+obj/dbg: override DEF := $(DEF) -D DEBUG 
+obj/dbg: zlib cleanobj obj/dbgdir $(OBJDBG)
+
+obj/dbg_de: override DEF := $(DEF) -D COLOR -D DEBUG
+obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
+
+obj/%.o: src/%.c
+	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
+
+obj/dbg/%.o: src/%.c
+	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
+
+doc: Manual.pdf
+
+Manual.pdf: doc/manual_src/Manual.tex doc/manual_src/Columbus_manual.tex
+ifdef PDFLATEX_VERSION
+	cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../..
+else
+	@echo pdflatex not found, cannot rebuild the manual.
+endif
+
+test: velvetg velveth
+	cd tests && ./run-tests.sh

data/ext/src/src/allocArray.c

@@ -0,0 +1,305 @@
+/*
+Copyright 2009 Sylvain Foret (sylvain.foret@anu.edu.au) 
+
+    This file is part of Velvet.
+
+    Velvet 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 2 of the License, or
+    (at your option) any later version.
+
+    Velvet 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 Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+#include "allocArray.h"
+#include "utility.h"
+
+#ifdef DEBUG
+#define NB_PAGES_ALLOC    1
+#define BLOCKS_ALLOC_SIZE 1
+#else
+#define NB_PAGES_ALLOC    128
+#define BLOCKS_ALLOC_SIZE 128
+#endif
+
+#ifndef VBIGASSEMBLY
+#define INDEX_LENGTH 32
+#else
+#define INDEX_LENGTH 64
+#endif
+
+struct AllocArrayFreeElement_st
+{
+	AllocArrayFreeElement *next;
+	ArrayIdx idx;
+};
+
+static void initAllocArray(AllocArray * array, size_t elementSize, char * name) 
+{
+	array->freeElements = NULL;
+	array->elementSize = elementSize;
+	array->blockSize = sysconf (_SC_PAGESIZE) * NB_PAGES_ALLOC;
+	array->maxElements = array->blockSize / array->elementSize;
+	array->maxBlocks = BLOCKS_ALLOC_SIZE;
+	array->blocks = mallocOrExit (array->maxBlocks, void*);
+	array->blocks[0] = mallocOrExit (array->blockSize, char);
+	array->currentBlocks = 1;
+	array->currentElements = 0;
+#ifdef DEBUG
+	array->elementsRecycled = 0;
+	array->elementsAllocated = 0;
+	array->name = name;
+#endif
+#ifdef _OPENMP
+	array->nbThreads = 0;
+#endif
+}
+
+AllocArray*
+newAllocArray (size_t elementSize, char *name)
+{
+	AllocArray *array;
+
+	if (elementSize < sizeof(AllocArrayFreeElement)) {
+		velvetLog("Elements too small to create an AllocArray!\n");
+		exit(-1);
+	}
+	array = mallocOrExit (1, AllocArray);
+	initAllocArray(array, elementSize, name);
+	return array;
+}
+
+void
+destroyAllocArrayChunks (AllocArray *array)
+{
+	size_t i;
+	for (i = 0; i < array->currentBlocks; i++)
+		free (array->blocks[i]);
+	free (array->blocks);
+}
+
+void
+destroyAllocArray (AllocArray *array)
+{
+	if (array)
+	{
+		destroyAllocArrayChunks(array);
+#ifdef DEBUG
+		velvetLog(">>> Allocation summary for %s\n", array->name);
+		velvetLog(">>> Alloc'ed %ld bytes\n", array->blockSize * array->currentBlocks);
+		velvetLog(">>> Alloc'ed %ld elements\n", array->elementsAllocated);
+		velvetLog(">>> Recycled %ld elements\n", array->elementsRecycled);
+#endif
+		free (array);
+	}
+}
+
+ArrayIdx
+allocArrayAllocate (AllocArray *array)
+{
+	if (array->freeElements != NULL)
+	{
+		AllocArrayFreeElement *element;
+
+		element = array->freeElements;
+		array->freeElements = element->next;
+#ifdef DEBUG
+		array->elementsRecycled++;
+#endif
+		return element->idx;
+	}
+	if (array->currentElements >= array->maxElements)
+	{
+		if (array->currentBlocks == array->maxBlocks)
+		{
+			array->maxBlocks += BLOCKS_ALLOC_SIZE;
+			array->blocks = reallocOrExit (array->blocks, array->maxBlocks, void*);
+		}
+		array->blocks[array->currentBlocks] = mallocOrExit (array->blockSize, char);
+		array->currentBlocks++;
+		array->currentElements = 0;
+	}
+	array->currentElements++;
+#ifndef VBIGASSEMBLY
+	if (array->maxElements * (array->currentBlocks - 1) + array->currentElements == UINT32_MAX)
+	{
+#ifdef DEBUG
+		velvetLog (">>> Reached maximum `%s' addressable with %i bits\n", array->name, INDEX_LENGTH);
+#else
+		velvetLog (">>> Reached maximum elements addressable with %i bits\n", INDEX_LENGTH);
+#endif
+		abort();
+	}
+#endif
+
+#ifdef DEBUG
+	array->elementsAllocated++;
+#endif
+
+	return array->maxElements * (array->currentBlocks - 1) + array->currentElements;
+}
+
+static void*
+allocArrayGetElement (AllocArray *array, ArrayIdx idx)
+{
+	if (idx != NULL_IDX)
+	{
+		const ArrayIdx i = idx - 1;
+		const ArrayIdx blockIdx = i / array->maxElements;
+		const ArrayIdx elementIdx = i % array->maxElements;
+		return ((char*)(array->blocks[blockIdx])) + elementIdx * array->elementSize;
+	}
+	return NULL;
+}
+
+void
+allocArrayFree (AllocArray *array, ArrayIdx idx)
+{
+	if (idx != NULL_IDX)
+	{
+		AllocArrayFreeElement *freeElem;
+
+		freeElem = allocArrayGetElement (array, idx);
+		freeElem->idx = idx;
+		freeElem->next = array->freeElements;
+		array->freeElements = freeElem;
+	}
+}
+
+#ifdef _OPENMP
+
+#define BLOCKS_ALLOC_SHIFT 16
+
+static void initAllocArrayArray(AllocArray *array,
+				void *blocks,
+				size_t nbBlocks,
+				size_t elementSize,
+				char *name,
+				int nbThreads,
+				int thisThread)
+{
+	array->freeElements = NULL;
+	array->elementSize = elementSize;
+	array->blockSize = (((size_t) 1) << BLOCKS_ALLOC_SHIFT) * elementSize;
+	array->maxElements = (((size_t) 1) << BLOCKS_ALLOC_SHIFT);
+	array->maxBlocks = nbBlocks;
+	array->blocks = blocks;
+	array->blocks[thisThread] = callocOrExit(array->blockSize, char);
+	array->currentBlocks = thisThread;
+	array->currentElements = 0;
+	array->nbThreads = nbThreads;
+#ifdef DEBUG
+	array->elementsRecycled = 0;
+	array->elementsAllocated = 0;
+	array->name = name;
+#endif
+}
+
+AllocArray *newAllocArrayArray(unsigned int n,
+			       size_t elementSize,
+			       char * name)
+{
+	AllocArray *allocArray;
+	void **blocks;
+	size_t nbBlocks;
+	int i;
+
+	allocArray = callocOrExit (n + 1, AllocArray);
+	nbBlocks = (((size_t) 1) << (INDEX_LENGTH - BLOCKS_ALLOC_SHIFT));
+	blocks = callocOrExit(nbBlocks, void*);
+	for (i = 0; i < n; i++)
+		initAllocArrayArray(allocArray + i,
+				    blocks,
+				    nbBlocks,
+				    elementSize,
+				    name,
+				    n, i);
+	/* Last element marker */
+	allocArray[n].currentBlocks = n;
+
+	return allocArray;
+}
+
+void destroyAllocArrayArray(AllocArray *allocArray)
+{
+	int i;
+
+	for (i = 0; i < allocArray[0].maxBlocks; i++)
+		if (allocArray[0].blocks[i] != NULL)
+			free(allocArray[0].blocks[i]);
+
+	free(allocArray[0].blocks);
+	free(allocArray);
+}
+
+ArrayIdx allocArrayArrayAllocate(AllocArray *array)
+{
+	int thread = omp_get_thread_num();
+
+	AllocArray * lastArray = array + array->nbThreads;
+	array += thread;
+	if (array->freeElements != NULL)
+	{
+		AllocArrayFreeElement *element;
+
+		element = array->freeElements;
+		array->freeElements = element->next;
+#ifdef DEBUG
+		array->elementsRecycled++;
+#endif
+		return element->idx;
+	}
+	if (array->currentElements >= array->maxElements)
+	{
+		#pragma omp critical 
+		array->currentBlocks = lastArray->currentBlocks++;
+
+		if (array->currentBlocks >= array->maxBlocks)
+		{
+#ifdef DEBUG
+			velvetLog(">>> Reached maximum `%s' addressable with %i bits\n",
+				  array->name, INDEX_LENGTH);
+#else
+			velvetLog(">>> Reached maximum elements addressable with %i bits\n", INDEX_LENGTH);
+#endif
+			abort();
+		}
+		array->blocks[array->currentBlocks] = callocOrExit(array->blockSize, char);
+		array->currentElements = 0;
+	}
+	array->currentElements++;
+#ifdef DEBUG
+	array->elementsAllocated++;
+#endif
+	return array->maxElements * array->currentBlocks + array->currentElements;
+}
+
+void
+allocArrayArrayFree(AllocArray *array, ArrayIdx idx)
+{
+	if (idx != NULL_IDX)
+	{
+		AllocArrayFreeElement *freeElem;
+
+		freeElem = allocArrayGetElement(array, idx);
+		freeElem->idx = idx;
+		freeElem->next = array->freeElements;
+		array->freeElements = freeElem;
+	}
+}
+#endif