gds::VariantSet Class Reference

#include <VariantSet.h>

Public Member Functions
	VariantSet ()
	VariantSet (const vector< string > &chrom, const vector< int > &position, const vector< string > &id=vector< string >())
vector< int >	getIndeces (const string &chrom, const int &start, const int &end)
vector< int >	getIndeces (const GenomicRanges &gr)
vector< string >	getVariantIDs () const
vector< string >	getVariantIDs (const vector< int > &idx) const
GenomicRanges	getChromRanges () const

Detailed Description

Store position and ID, sorted by position. Get indeces of variants with a query interval using binary search in O(log(N)) time.

Constructor & Destructor Documentation

VariantSet() [1/2]

gds::VariantSet::VariantSet ( )

inline

VariantSet() [2/2]

gds::VariantSet::VariantSet ( const vector< string > & chrom, const vector< int > & position, const vector< string > & id = vector<string>() )

inline

Member Function Documentation

getChromRanges()

GenomicRanges gds::VariantSet::getChromRanges ( ) const

inline

getIndeces() [1/2]

vector< int > gds::VariantSet::getIndeces ( const GenomicRanges & gr )

inline

Get indeces of variants within set of query intervals. Use binary search for each interval

getIndeces() [2/2]

vector< int > gds::VariantSet::getIndeces ( const string & chrom, const int & start, const int & end )

inline

Get indeces of variants within the query interval using binary search

getVariantIDs() [1/2]

vector< string > gds::VariantSet::getVariantIDs ( ) const

inline

getVariantIDs() [2/2]

vector< string > gds::VariantSet::getVariantIDs ( const vector< int > & idx ) const

inline

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

• inst/include/VariantSet.h