SortingCountAlgorithm< span > Class Template Reference

Class performing the kmer counting (also known as 'DSK') More...

#include <SortingCountAlgorithm.hpp>

Inheritance diagram for SortingCountAlgorithm< span >:

Public Member Functions
	SortingCountAlgorithm (tools::misc::IProperties *params=0)
	SortingCountAlgorithm (gatb::core::bank::IBank *bank, tools::misc::IProperties *params)
	SortingCountAlgorithm (gatb::core::bank::IBank *bank, const Configuration &config, Repartitor *repartitor, std::vector< CountProcessor * > processors, tools::misc::IProperties *params)
virtual	~SortingCountAlgorithm ()
SortingCountAlgorithm &	operator= (const SortingCountAlgorithm &s)
void	execute ()
size_t	getProcessorNumber () const
CountProcessor *	getProcessor (size_t idx)
void	addProcessor (CountProcessor *processor)
tools::storage::impl::Partition< Count > *	getSolidCounts ()
tools::collections::Iterable< Type > *	getSolidKmers ()
const kmer::impl::Configuration &	getConfig () const
Repartitor *	getRepartitor ()
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 (bool mandatory=true)
static tools::misc::IProperties *	getDefaultProperties ()
static CountProcessor *	getDefaultProcessor (tools::misc::IProperties *params, tools::storage::impl::Storage *dskStorage, tools::storage::impl::Storage *otherStorage=0)
static std::vector< ICountProcessor< span > * >	getDefaultProcessorVector (Configuration &config, tools::misc::IProperties *params, tools::storage::impl::Storage *dskStorage, tools::storage::impl::Storage *otherStorage=0)
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::SortingCountAlgorithm< span >

Class performing the kmer counting (also known as 'DSK')

This class does the real job of counting the kmers from a reads database.

This is a template class whose template argument is the kind of integer used for kmers (integers on 64 bits, 128 bits, etc...)

We define some template instantiations of this SortingCountAlgorithm; such an instantiation does the real job of kmers counting. By defining several instantiations, we allow to choose dynamically the correct class according to the user choice for kmer size (remember that initial Minia version had to be re-compiled for different kmer size).

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

Constructor & Destructor Documentation

SortingCountAlgorithm

(

tools::misc::IProperties *

params = 0

)

Constructor. Can be used as default constructor in no parameters are provided

Parameters

[in]

params

: parameters to be used for configuring the algorithm

SortingCountAlgorithm	(	gatb::core::bank::IBank *	bank,
		tools::misc::IProperties *	params
	)

Constructor.

Parameters

[in]	bank	: input bank from which solid kmers are counted
[in]	params	: parameters to be used for configuring the algorithm

SortingCountAlgorithm	(	gatb::core::bank::IBank *	bank,
		const Configuration &	config,
		Repartitor *	repartitor,
		std::vector< CountProcessor * >	processors,
		tools::misc::IProperties *	params
	)

Constructor.

Parameters

[in]	bank	: input bank from which solid kmers are counted
[in]	config	: configuration information
[in]	repartitor	: hash function for minimizers
[in]	processor	: object that processes counts

~SortingCountAlgorithm ( )

virtual

Destructor

Member Function Documentation

void addProcessor ( CountProcessor *  processor )

inline

Setter for the CountProcessor to be used by the algorithm.

Parameters

[in]

processor

: the count processor to be used.

void execute ( )

virtual

Process the kmers counting. It is mainly composed of a loop over the passes, and for each pass : 1) we build the partition files then 2) we fill the solid kmers file from the partitions.

Implements Algorithm.

const kmer::impl::Configuration& getConfig ( ) const

inline

Get the configuration object for the algorithm.

Returns

the Configuration object.

ICountProcessor< span > * getDefaultProcessor ( tools::misc::IProperties *  params, tools::storage::impl::Storage *  dskStorage, tools::storage::impl::Storage *  otherStorage = 0  )

static

Creates a default CountProcessor instance (ie. the default one used by DSK)

Parameters

[in]	params	: used for configuring the processor
[in]	dskStorage	: storage for dumping [kmer,count] couples
[in]	otherStorage	: used for histogram for instance

Returns

a CountProcessor instance

vector< ICountProcessor< span > * > getDefaultProcessorVector ( Configuration &  config, tools::misc::IProperties *  params, tools::storage::impl::Storage *  dskStorage, tools::storage::impl::Storage *  otherStorage = 0  )

static

Creates a vector holding the default CountProcessor configuration

Parameters

[in]	params	: used for configuring the processor
[in]	dskStorage	: storage for dumping [kmer,count] couples
[in]	otherStorage	: used for histogram for instance

Returns

a vector of CountProcessor instances

IProperties * getDefaultProperties ( )

static

Get the default values defined in the default option parser.

Returns

default properties.

IOptionsParser * getOptionsParser ( bool  mandatory = true )

static

Get an option parser for kmers counting parameters. Dynamic allocation, so must be released when no more used.

Parameters

[in]

mandatory

: tells whether an argument has to be mandatory

Returns

an instance of IOptionsParser.

CountProcessor* getProcessor ( size_t  idx )

inline

Getter for the CountProcessor to be used by the algorithm.

Parameters

[in]

idx

: index of the processor to be retrieved

Returns

the processor

size_t getProcessorNumber ( ) const

inline

Get the number of count processors associated to the object.

Returns

number of processors.

Repartitor* getRepartitor ( )

inline

Get the repartitor instance, ie. the hash function built on minimizer information.

Returns

the Repartitor instance

Partition< typename SortingCountAlgorithm< span >::Count > * getSolidCounts

(

)

Get the iterable over the computed solid kmers.

Returns

the solid kmers iterable.

Iterable< typename SortingCountAlgorithm< span >::Type > * getSolidKmers

(

)

Get the iterable over the computed solid kmers.

Returns

the solid kmers iterable.

SortingCountAlgorithm< span > & operator=

(

const SortingCountAlgorithm< span > &

s

)

operator=

Parameters

[in]

s

: object to be copied.

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