DebloomAlgorithm< span > Class Template Reference

Construction of the set of critical false positives nodes. More...

#include <DebloomAlgorithm.hpp>

Inheritance diagram for DebloomAlgorithm< span >:

Public Types
typedef kmer::impl::Kmer< span >::ModelCanonical	Model

Public Member Functions
	DebloomAlgorithm (tools::storage::impl::Group &bloomGroup, tools::storage::impl::Group &debloomGroup, tools::storage::impl::Partition< Count > *solidIterable, size_t kmerSize, size_t miniSize, size_t max_memory=0, size_t nb_cores=0, tools::misc::BloomKind bloomKind=tools::misc::BLOOM_DEFAULT, tools::misc::DebloomKind debloomKind=tools::misc::DEBLOOM_DEFAULT, const std::string &debloomUri="debloom", tools::misc::IProperties *options=0)
	DebloomAlgorithm (tools::storage::impl::Storage &storage)
virtual	~DebloomAlgorithm ()
void	execute ()
tools::collections::Collection< Type > *	getCriticalKmers ()
debruijn::IContainerNode< Type > *	getContainerNode ()
virtual const char *	getClassName () const
Public Member Functions inherited from Algorithm
	Algorithm (const std::string &name, int nbCores=-1, gatb::core::tools::misc::IProperties *input=0)
virtual	~Algorithm ()
std::string	getName () const
void	run ()
virtual IProperties *	getInput ()
virtual IProperties *	getOutput ()
virtual IProperties *	getInfo ()
virtual dp::IDispatcher *	getDispatcher ()
virtual TimeInfo &	getTimeInfo ()
virtual IProperties *	getSystemInfo ()
template<typename Item >
dp::Iterator< Item > *	createIterator (dp::Iterator< Item > *iter, size_t nbIterations=0, const char *message=0, dp::IteratorListener *listener=0)
virtual dp::IteratorListener *	createIteratorListener (size_t nbIterations, const char *message)
Public Member Functions inherited from SmartPointer
void	use ()
void	forget ()
Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()

Static Public Member Functions
static tools::misc::IOptionsParser *	getOptionsParser ()
static float	getNbBitsPerKmer (size_t kmerSize, tools::misc::DebloomKind debloomKind)
Static Public Member Functions inherited from Algorithm
template<template< size_t > class Functor>
static int	mainloop (tools::misc::IOptionsParser *parser, int argc, char *argv[])

Additional Inherited Members
Protected Member Functions inherited from Algorithm
std::string	getUriByKey (const std::string &key)
std::string	getUri (const std::string &str)
void	setInput (IProperties *input)
Protected Member Functions inherited from SmartPointer
	SmartPointer ()
virtual	~SmartPointer ()

Detailed Description

template<size_t span = KMER_DEFAULT_SPAN>
class gatb::core::kmer::impl::DebloomAlgorithm< span >

Construction of the set of critical false positives nodes.

GATB uses Bloom filters for encoding de Bruijn graphs. Since Bloom filters are probalistic data structure having false positives, we need extra information for disambiguate the graph, otherwise we would have false positive nodes in our de Bruijn graphs.

It is possible to build this extra information as a set of critical false positives nodes and the DebloomAlgorithm class provides a way to build such cFP set.

Actually, this class is mainly used in the debruijn::impl::Graph class as a third step for the de Bruijn graph creation.

Member Typedef Documentation

typedef kmer::impl::Kmer<span>::ModelCanonical Model

Shortcuts.

Constructor & Destructor Documentation

DebloomAlgorithm	(	tools::storage::impl::Group &	bloomGroup,
		tools::storage::impl::Group &	debloomGroup,
		tools::storage::impl::Partition< Count > *	solidIterable,
		size_t	kmerSize,
		size_t	miniSize,
		size_t	max_memory = 0,
		size_t	nb_cores = 0,
		tools::misc::BloomKind	bloomKind = tools::misc::BLOOM_DEFAULT,
		tools::misc::DebloomKind	debloomKind = tools::misc::DEBLOOM_DEFAULT,
		const std::string &	debloomUri = "debloom",
		tools::misc::IProperties *	options = 0
	)

Constructor

Parameters

[in]	storage	: storage object where the cFP will be stored.
[in]	storageSolids	: obsolete (should be removed)
[in]	solidIterable	: partition holding the solid kmers
[in]	kmerSize	: size of the kmers
[in]	max_memory	: max memory (in MBytes) to be used
[in]	nb_cores	: number of cores to be used; 0 means all available cores
[in]	bloomKind	: kind of Bloom filter implementation to be used
[in]	debloomKind	: kind of algorithm to be used for storing the cFP
[in]	debloomUri	: prefix name for temporary files
[in]	options	: extra options

DebloomAlgorithm

(

tools::storage::impl::Storage &

storage

)

Constructor

Parameters

[in]

storage

: storage object from which the cFP can be loaded.

~DebloomAlgorithm ( )

virtual

Destructor

Member Function Documentation

void execute ( )

virtual

Execute the debloom algorithm.

Implements Algorithm.

virtual const char* getClassName ( ) const

inlinevirtual

Get the class name (for statistics output).

Returns

the class name.

debruijn::IContainerNode<Type>* getContainerNode ( )

inline

Get the bloom/cFP container.

Returns

the container.

tools::collections::Collection<Type>* getCriticalKmers ( )

inline

Get the collection for the computed critical FP kmers.

Returns

the cFP kmers collection.

float getNbBitsPerKmer ( size_t  kmerSize, tools::misc::DebloomKind  debloomKind  )

static

Get the number of bits per kmer

Parameters

[in]	kmerSize	: kmer size
[in]	debloomKind	: kind of debloom

Returns

number of bits per kmer.

IOptionsParser * getOptionsParser ( )

static

Get an option parser for bloom/debloom parameters. Dynamic allocation, so must be released when no more used.

Returns

an instance of IOptionsParser.

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The documentation for this class was generated from the following files:

• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.hpp
• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp