SVData Class Reference

#include <sv_data.h>

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Public Member Functions
	SVData (FASTAQuery &ref_genome)
void	addSVCall (std::string chr, int start, int end, int sv_type, std::string alt_allele)
std::string	getRefGenome ()
std::string	getSequence (std::string chr, int pos_start, int pos_end)
void	updateSVType (SVCandidate key, int sv_type)
void	saveToVCF (FASTAQuery &ref_genome, std::string output_dir)
SVDepthMap::iterator	begin ()
SVDepthMap::iterator	end ()

Private Attributes
SVDepthMap	sv_calls
FASTAQuery *	ref_genome
std::map< int, std::string >	sv_type_map

Constructor & Destructor Documentation

SVData()

SVData::SVData

(

FASTAQuery &

ref_genome

)

Member Function Documentation

addSVCall()

void SVData::addSVCall	(	std::string	chr,
		int	start,
		int	end,
		int	sv_type,
		std::string	alt_allele
	)

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begin()

SVDepthMap::iterator SVData::begin ( )

inline

end()

SVDepthMap::iterator SVData::end ( )

inline

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getRefGenome()

std::string SVData::getRefGenome

(

)

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getSequence()

std::string SVData::getSequence	(	std::string	chr,
		int	pos_start,
		int	pos_end
	)

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saveToVCF()

void SVData::saveToVCF	(	FASTAQuery &	ref_genome,
		std::string	output_dir
	)

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updateSVType()

void SVData::updateSVType	(	SVCandidate	key,
		int	sv_type
	)

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Member Data Documentation

ref_genome

FASTAQuery* SVData::ref_genome

private

sv_calls

SVDepthMap SVData::sv_calls

private

sv_type_map

std::map<int, std::string> SVData::sv_type_map

private

Initial value:

= {
            {0, "DEL"},
            {1, "DUP"},
            {2, "INV"},
            {3, "INS"},
            {4, "BND"}
        }

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

• include/sv_data.h
• src/sv_data.cpp