gds::vcfstream Class Reference

#include <vcfstream.h>

Inheritance diagram for gds::vcfstream:

Public Member Functions
	vcfstream ()
	vcfstream (const Param &param)
	~vcfstream () override
void	setRegions (const vector< string > &regions) override
int	n_samples () override
vector< string >	getSampleNames () override
string	getStreamType () override
GenomicRanges	getChromRanges () override
bool	getNextChunk (DataChunk< arma::mat > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< arma::sp_mat > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< Eigen::MatrixXd > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< Eigen::SparseMatrix< double > > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< Rcpp::NumericMatrix > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< vector< double > > &chunk, const bool &useFilter=true) override
Public Member Functions inherited from gds::GenomicDataStream
	GenomicDataStream ()
	GenomicDataStream (const Param &param)
virtual	~GenomicDataStream ()
double	getMinVariance ()
double	getMAF () const
void	setMinVariance (const double &value)
void	setChunkSize (const int &chunkSize)
Param	getParam () const

Static Public Member Functions
static string	variantToString (const BcfRecord &record)

Additional Inherited Members
Protected Attributes inherited from gds::GenomicDataStream
Param	param

Detailed Description

vcfstream reads a VCF/BCF into an matrix in chunks, storing variants in columns. Applies filtering for specified samples and genome region.

Constructor & Destructor Documentation

vcfstream() [1/2]

gds::vcfstream::vcfstream ( )

inline

vcfstream() [2/2]

gds::vcfstream::vcfstream ( const Param & param )

inline

constructor initilizing with parameter values

~vcfstream()

gds::vcfstream::~vcfstream ( )

inlineoverride

destructor

Member Function Documentation

getChromRanges()

GenomicRanges gds::vcfstream::getChromRanges ( )

inlineoverridevirtual

Get maximum position for each chrom

Implements gds::GenomicDataStream.

getNextChunk() [1/6]

bool gds::vcfstream::getNextChunk ( DataChunk< arma::mat > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as arma::mat

Implements gds::GenomicDataStream.

getNextChunk() [2/6]

bool gds::vcfstream::getNextChunk ( DataChunk< arma::sp_mat > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as arma::sp_mat

Implements gds::GenomicDataStream.

getNextChunk() [3/6]

bool gds::vcfstream::getNextChunk ( DataChunk< Eigen::MatrixXd > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as Eigen::MatrixXd

Implements gds::GenomicDataStream.

getNextChunk() [4/6]

bool gds::vcfstream::getNextChunk ( DataChunk< Eigen::SparseMatrix< double > > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as SparseMatrix<double>

Implements gds::GenomicDataStream.

getNextChunk() [5/6]

bool gds::vcfstream::getNextChunk ( DataChunk< Rcpp::NumericMatrix > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as Rcpp::NumericMatrix

Implements gds::GenomicDataStream.

getNextChunk() [6/6]

bool gds::vcfstream::getNextChunk ( DataChunk< vector< double > > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as vector<double>

Implements gds::GenomicDataStream.

getSampleNames()

vector< string > gds::vcfstream::getSampleNames ( )

inlineoverridevirtual

Get vector of sample names in order that the genotypes are extracted

Implements gds::GenomicDataStream.

getStreamType()

string gds::vcfstream::getStreamType ( )

inlineoverridevirtual

get FileType of param.file

Implements gds::GenomicDataStream.

n_samples()

int gds::vcfstream::n_samples ( )

inlineoverridevirtual

Get number of columns in data matrix

Implements gds::GenomicDataStream.

setRegions()

void gds::vcfstream::setRegions ( const vector< string > & regions )

inlineoverridevirtual

setter

Implements gds::GenomicDataStream.

variantToString()

string gds::vcfstream::variantToString ( const BcfRecord & record )

inlinestatic

Concatenate variant identifiers

Parameters

record

storing current variant

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

• inst/include/vcfstream.h