GenomicDataStream
A scalable interface between data and analysis
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Public Member Functions | Protected Attributes | List of all members
gds::GenomicDataStream Class Referenceabstract

#include <GenomicDataStream_virtual.h>

Inheritance diagram for gds::GenomicDataStream:
gds::DelayedStream gds::bgenstream gds::pgenstream gds::vcfstream

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
The documentation for this class was generated from the following file:
Generated by doxygen 1.14.0