finishm 0.0.1

data/bin/scaffold_end_coverages.rb

@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'bio-logger'
+require 'bio-samtools'
+require 'bio'
+
+if __FILE__ == $0 #needs to be removed if this script is distributed as part of a rubygem
+  SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+
+  # Parse command line options into the options hash
+  options = {
+    :logger => 'stderr',
+    :contig_end_length => 200,
+  }
+  o = OptionParser.new do |opts|
+    opts.banner = "
+      Usage: #{SCRIPT_NAME} <arguments>
+
+      Takes a sorted, indexed BAM file and outputs the coverages of each of the reference sequences\n\n"
+
+    opts.on("-b", "--bam BAM_FILE", "BAM file that defines overall mapping/coverage [required]") do |arg|
+      options[:bam_file] = arg
+    end
+    opts.on("-f", "--reference-fasta FASTA_FILE", "FASTA file of the reference [required]") do |arg|
+      options[:fasta_file] = arg
+    end
+
+    opts.on("-l", "--end-length LENGTH", "How far from the end to count [default: #{options[:contig_end_length]}]") do |arg|
+      options[:contig_end_length] = arg.to_i
+      raise "Inappropriate end length detected, I need a positive number, found #{options[:contig_end_length]} parsed from #{arg}" if options[:contig_end_length] < 1
+    end
+
+    # logger options
+    opts.separator "\n\tVerbosity:\n\n"
+    opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {Bio::Log::CLI.trace('error')}
+    opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
+    opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| Bio::Log::CLI.trace(s)}
+  end; o.parse!
+  if ARGV.length != 0 or options[:bam_file].nil? or options[:fasta_file].nil?
+    $stderr.puts o
+    exit 1
+  end
+  # Setup logging. bio-logger defaults to STDERR not STDOUT, I disagree
+  Bio::Log::CLI.logger(options[:logger]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
+
+
+  # open the BAM file for reading
+  bam = Bio::DB::Sam.new(:bam => options[:bam_file], :fasta => options[:fasta_file])
+  bam.open
+  puts %w(Reference StartCoverage EndCoverage).join("\t")
+  contigs_file = Bio::FlatFile.auto(options[:fasta_file])
+  contigs_file.each_entry do |record|
+    ref = record.definition
+    ref_length = record.length
+  #bam.each_reference do |ref, ref_length| #currently commented out because there is extraneous output on STDOUT if you use this
+    next if ref == '*' #Ignore umapped reads
+    # Coverage of the start
+    end_length = options[:contig_end_length]
+    end_length = ref_length if ref_length < options[:contig_end_length]
+
+    cov_start = bam.average_coverage(ref, 1, end_length)
+    cov_end = bam.average_coverage(ref, ref_length-end_length+1, end_length)
+    puts [
+      ref, cov_start, cov_end
+    ].join("\t")
+  end
+  exit
+end #end if running as a script

data/bin/trail_validator.rb

@@ -0,0 +1,84 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'bio-logger'
+require 'pp'
+
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = 'finishm'
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+require 'priner'
+
+# Parse command line options into the options hash
+options = {
+  :logger => 'stderr',
+  :log_level => 'info',
+}
+
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} --trails <trail(s) fasta> --kmer-abundances <abundances.csv>
+
+    Given an input kmer set of sequences then abundances space separated file, and a threshold, print out how many kmers are unique to different subsets of columns\n\n"
+
+  opts.on("--trails FASTA_FILE", "fasta file of trail(s) to be tested [required]") do |arg|
+    options[:trails_fasta_file] = arg
+  end
+  opts.on("--kmer-abundances FILE", "kmer multiple abundance file [required]") do |arg|
+    options[:kmer_multiple_abundance_file] = arg
+  end
+
+  #opts.separator "\nOptional arguments:\n\n"
+  opts.on("--output-kmer-coverages FILE", "output kmer coverages across each library across the contigs default: don't output]") do |arg|
+    options[:output_trail_kmer_coverage_file] = arg
+  end
+
+  # logger options
+  opts.separator "\nVerbosity:\n\n"
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
+end; o.parse!
+if ARGV.length != 0 or options[:trails_fasta_file].nil? or options[:kmer_multiple_abundance_file].nil? or options[:output_trail_kmer_coverage_file].nil?
+  $stderr.puts "Options not correctly specified. Found:"
+  pp options
+  $stderr.puts o
+  exit 1
+end
+# Setup logging
+Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
+
+# read in fasta file of trails
+log.info "Reading trail sequences from #{options[:trails_fasta_file]}"
+fasta_seqs = {}
+Bio::FlatFile.foreach(options[:trails_fasta_file]) do |e|
+  name = e.definition
+  seq = e.seq.seq
+  fasta_seqs[name]=seq
+end
+
+log.info "Reading kmer abundances from #{options[:kmer_multiple_abundance_file]}.."
+kmer_hash = Bio::KmerMultipleAbundanceHash.parse_from_file options[:kmer_multiple_abundance_file]
+log.info "Finished reading the kmer abundances"
+
+if options[:output_trail_kmer_coverage_file]
+  log.info "Writing out kmer coverages to #{options[:output_trail_kmer_coverage_file]}.."
+  writer = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new
+  io = File.open(options[:output_trail_kmer_coverage_file],'w')
+  fasta_seqs.each do |name, seq|
+    log.debug "Writing coverages for #{name}"
+    writer.write_depths(io, name, seq, kmer_hash)
+  end
+  log.info "Finished writing"
+end
+
+#log.info "Filtering trail(s) based on kmer coverage, requiring each kmer in the path to have a minimum of #{options[:kmer_path_filter_min_coverage]} coverage in patterned reads, except for the #{options[:kmer_path_end_exclusion_length]}bp at the ends"
+#kmer_path_filter = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new
+#thresholds = desired_pattern.collect{|c| c == true ? 1 : 0}
+#log.info "Using thresholds for filtering: #{thresholds}"
+#trails = kmer_path_filter.filter(trails, kmer_hash, thresholds, :exclude_ending_length => options[:kmer_path_end_exclusion_length])
+#log.info "After filtering remained #{trails.length} trails"
+
+#trails.each_with_index do |trail, i|
+#  puts ">trail#{i+1}"
+#  puts trail.sequence
+#end

data/ext/mkrf_conf.rb

@@ -0,0 +1,56 @@
+#(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/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/external")
+
+task :compile do
+  cd(File.join(File.dirname(__FILE__),'src')) do
+    #sh "patch -p1 < ../bioruby.patch"
+    case Config::CONFIG['host_os']
+      when /linux/
+
+        # Create library with default install params
+        $stdout.puts "Making velvet shared library with default parameters"
+        sh "make MAXKMERLENGTH=255 finishm velveth velvetg"
+        $stdout.puts "Finished make finishm"
+        shared_location = 'obj/shared'
+        cp(File.join(shared_location,"libfinishm.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 +1,140 @@
+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 obj/probe_node_finder.o obj/readToNode.o obj/runReadToNode.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* obj/shared/*.o
+	-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 obj/shared/*.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 obj/readToNode.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
+
+sharedobjdir:
+	mkdir -p obj/shared
+
+obj/shared: sharedobjdir $(OBJSHARED)
+
+obj/shared/%.o: src/%.c
+	$(CC) -fPIC $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
+
+finishm: zlib obj/shared
+	cd obj/shared && gcc -shared -Wl,-soname,libfinishm.so.1 -o libfinishm.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 probe_node_finder.o readToNode.o
+
+readToNodeBinary: obj
+	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o readToNode obj/runReadToNode.o obj/tightString.o obj/graph.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 obj/readToNode.o $(Z_LIB_FILES) $(LIBS)

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