This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF). More...

Inheritance diagram for bpp::VcfOutputMafIterator:

Collaboration diagram for bpp::VcfOutputMafIterator:

Public Member Functions
	VcfOutputMafIterator (MafIterator iterator, std::ostream out, const std::string &reference, const std::vector< std::string > &genotypes, bool outputAll=false, bool generateDiploids=false)
	Build a new VcfOutputMafIterator object. More...

	VcfOutputMafIterator (MafIterator iterator, std::ostream out, const std::string &reference, const std::vector< std::vector< std::string > > &genotypes, bool outputAll=false)
	Build a new VcfOutputMafIterator object. More...

MafBlock *	analyseCurrentBlock_ ()

void	setLogStream (std::shared_ptr< OutputStream > logstream)

void	addIterationListener (IterationListener *listener)

MafBlock *	nextBlock ()
	Get the next available alignment block. More...

bool	isVerbose () const

void	setVerbose (bool yn)

Protected Member Functions
virtual void	fireIterationStartSignal_ ()

virtual void	fireIterationMoveSignal_ (const MafBlock &currentBlock)

virtual void	fireIterationStopSignal_ ()

Protected Attributes
MafIterator *	iterator_

MafBlock *	currentBlock_

std::shared_ptr< OutputStream >	logstream_

std::vector< IterationListener * >	iterationListeners_

bool	started_

bool	verbose_

Private Member Functions
	VcfOutputMafIterator (const VcfOutputMafIterator &iterator)

VcfOutputMafIterator &	operator= (const VcfOutputMafIterator &iterator)

void	writeHeader_ (std::ostream &out) const

void	writeBlock_ (std::ostream &out, const MafBlock &block) const

Private Attributes
std::ostream *	output_

std::string	refSpecies_

std::vector< std::vector< std::string > >	genotypes_

bool	outputAll_

bool	generateDiploids_

Detailed Description

This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF).

Only substitutions are supported for now.

Definition at line 57 of file VcfOutputMafIterator.h.

Constructor & Destructor Documentation

bpp::VcfOutputMafIterator::VcfOutputMafIterator	(	MafIterator *	iterator,
		std::ostream *	out,
		const std::string &	reference,
		const std::vector< std::string > &	genotypes,
		bool	outputAll = `false`,
		bool	generateDiploids = `false`
	)

inline

Parameters

iterator	The input iterator.
out	The output stream where to write the VCF file.
reference	The species to use as a reference.
genotypes	A list of species for which genotype information should be written in the VCF file. There will be one extra column per genotype, +1 format column.
outputAll	If true, also output non-variable positions.
generateDiploids	If true, output artificial "homozygous" diploids.

Definition at line 78 of file VcfOutputMafIterator.h.

bpp::VcfOutputMafIterator::VcfOutputMafIterator	(	MafIterator *	iterator,
		std::ostream *	out,
		const std::string &	reference,
		const std::vector< std::vector< std::string > > &	genotypes,
		bool	outputAll = `false`
	)

inline

Parameters

iterator	The input iterator.
out	The output stream where to write the VCF file.
reference	The species to use as a reference.
genotypes	A list of species combinations for which genotype information should be written in the VCF file. There will be one extra column per genotype, +1 format column. When more than one sequence is specified in a combination, a (phased) polyploid genotype will be created.
outputAll	If true, also output non-variable positions.