gds::GenomicDataStream Class Reference

#include <GenomicDataStream_virtual.h>

Inheritance diagram for gds::GenomicDataStream:

Public Member Functions
	GenomicDataStream ()
	GenomicDataStream (const Param &param)
virtual	~GenomicDataStream ()
virtual void	setRegions (const vector< string > &regions)=0
virtual int	n_samples ()=0
virtual vector< string >	getSampleNames ()=0
virtual string	getStreamType ()=0
virtual GenomicRanges	getChromRanges ()=0
double	getMinVariance ()
double	getMAF () const
void	setMinVariance (const double &value)
void	setChunkSize (const int &chunkSize)
Param	getParam () const
virtual bool	getNextChunk (DataChunk< arma::mat > &chunk, const bool &useFilter=true)=0
virtual bool	getNextChunk (DataChunk< arma::sp_mat > &chunk, const bool &useFilter=true)=0
virtual bool	getNextChunk (DataChunk< Eigen::MatrixXd > &chunk, const bool &useFilter=true)=0
virtual bool	getNextChunk (DataChunk< Eigen::SparseMatrix< double > > &chunk, const bool &useFilter=true)=0
virtual bool	getNextChunk (DataChunk< Rcpp::NumericMatrix > &chunk, const bool &useFilter=true)=0
virtual bool	getNextChunk (DataChunk< vector< double > > &chunk, const bool &useFilter=true)=0

Protected Attributes
Param	param

Detailed Description

Virtual class inheritited by vcfstream, bgenstream, DelayedStream

Constructor & Destructor Documentation

GenomicDataStream() [1/2]

gds::GenomicDataStream::GenomicDataStream ( )

inline

GenomicDataStream() [2/2]

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

inline

Constructor

~GenomicDataStream()

virtual gds::GenomicDataStream::~GenomicDataStream ( )

inlinevirtual

destructor

Member Function Documentation

getChromRanges()

virtual GenomicRanges gds::GenomicDataStream::getChromRanges ( )

pure virtual

Get maximum position for each chrom

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getMAF()

double gds::GenomicDataStream::getMAF ( ) const

inline

get minVariance stored in Param

getMinVariance()

double gds::GenomicDataStream::getMinVariance ( )

inline

get minVariance stored in Param

getNextChunk() [1/6]

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

pure virtual

Get next chunk of features as arma::mat

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getNextChunk() [2/6]

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

pure virtual

Get next chunk of features as arma::sp_mat

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getNextChunk() [3/6]

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

pure virtual

Get next chunk of features as Eigen::MatrixXd

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getNextChunk() [4/6]

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

pure virtual

Get next chunk of features as SparseMatrix<double>

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getNextChunk() [5/6]

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

pure virtual

Get next chunk of features as Rcpp::NumericMatrix

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getNextChunk() [6/6]

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

pure virtual

Get next chunk of features as vector<double>

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getParam()

Param gds::GenomicDataStream::getParam ( ) const

inline

getSampleNames()

virtual vector< string > gds::GenomicDataStream::getSampleNames ( )

pure virtual

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

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

getStreamType()

virtual string gds::GenomicDataStream::getStreamType ( )

pure virtual

get FileType of param.file

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

n_samples()

virtual int gds::GenomicDataStream::n_samples ( )

pure virtual

Get number of columns in data matrix

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

setChunkSize()

void gds::GenomicDataStream::setChunkSize ( const int & chunkSize )

inline

setMinVariance()

void gds::GenomicDataStream::setMinVariance ( const double & value )

inline

set minVariance

setRegions()

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

pure virtual

setter

Implemented in gds::bgenstream, gds::DelayedStream, gds::pgenstream, and gds::vcfstream.

Member Data Documentation

param

Param gds::GenomicDataStream::param

protected

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

• inst/include/GenomicDataStream_virtual.h