gds::VariantInfo Class Reference

#include <VariantInfo.h>

Inheritance diagram for gds::VariantInfo:

Public Member Functions
	VariantInfo ()
	VariantInfo (const vector< string > &sampleNames)
void	addVariant (const string &chr, const int &pos, const string &id, const string &allele1, const string &allele2)
void	addVariants (const vector< string > &chr, const vector< string > &pos, const vector< string > &id, const vector< string > &allele1, const vector< string > &allele2)
void	append (const VariantInfo &vInfo)
void	retainVariants (const vector< unsigned int > &idx)
void	clear ()
string	getInterval () const
vector< string >	getRegions () const
vector< string >	getChromPos () const
int	getNVariantsBeforeFilter () const
Public Member Functions inherited from gds::DataInfo
	DataInfo ()
	DataInfo (const vector< string > &ID)
vector< string >	getFeatureNames () const
string	getFeatureName (const int &i) const
int	size () const

Public Attributes
vector< string >	sampleNames
vector< string >	CHROM
vector< int >	POS
vector< string >	A1
vector< string >	A2
int	nVariantsBeforeFilter = 0

Additional Inherited Members
Protected Attributes inherited from gds::DataInfo
vector< string >	ID

Detailed Description

Store variant information and sample names

Constructor & Destructor Documentation

VariantInfo() [1/2]

gds::VariantInfo::VariantInfo ( )

inline

VariantInfo() [2/2]

gds::VariantInfo::VariantInfo ( const vector< string > & sampleNames )

inline

constructor to intitialize sampleNames

Parameters

sampleNames

retained samples after filtering

Member Function Documentation

addVariant()

void gds::VariantInfo::addVariant ( const string & chr, const int & pos, const string & id, const string & allele1, const string & allele2 )

inline

add information for one variant at a time

addVariants()

void gds::VariantInfo::addVariants ( const vector< string > & chr, const vector< string > & pos, const vector< string > & id, const vector< string > & allele1, const vector< string > & allele2 )

inline

add information for many variant at a time

append()

void gds::VariantInfo::append ( const VariantInfo & vInfo )

inline

append variants in a new VariantInfo to the end of the current object

clear()

void gds::VariantInfo::clear ( )

inline

Clear vectors storing variant information, but leave sampleNames

getChromPos()

vector< string > gds::VariantInfo::getChromPos ( ) const

inline

get genomic regions as vector

getInterval()

string gds::VariantInfo::getInterval ( ) const

inline

get genome interval as a string

getNVariantsBeforeFilter()

int gds::VariantInfo::getNVariantsBeforeFilter ( ) const

inline

getRegions()

vector< string > gds::VariantInfo::getRegions ( ) const

inline

get genomic regions as vector

retainVariants()

void gds::VariantInfo::retainVariants ( const vector< unsigned int > & idx )

inline

Retain only variants with indeces stored in idx

Member Data Documentation

A1

vector<string> gds::VariantInfo::A1

A2

vector<string> gds::VariantInfo::A2

CHROM

vector<string> gds::VariantInfo::CHROM

nVariantsBeforeFilter

int gds::VariantInfo::nVariantsBeforeFilter = 0

POS

vector<int> gds::VariantInfo::POS

sampleNames

vector<string> gds::VariantInfo::sampleNames

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

• inst/include/VariantInfo.h