ReferenceGenome Class Reference

#include <fasta_query.h>

Collaboration diagram for ReferenceGenome:

Public Member Functions
	ReferenceGenome (std::shared_mutex &shared_mutex)
int	setFilepath (std::string fasta_filepath)
std::string	getFilepath () const
std::string_view	query (const std::string &chr, uint32_t pos_start, uint32_t pos_end) const
bool	compare (const std::string &chr, uint32_t pos_start, uint32_t pos_end, const std::string &compare_seq, float match_threshold) const
std::string	getContigHeader () const
std::vector< std::string >	getChromosomes () const
uint32_t	getChromosomeLength (std::string chr) const

Constructor & Destructor Documentation

ReferenceGenome()

ReferenceGenome::ReferenceGenome ( std::shared_mutex &  shared_mutex )

inline

Member Function Documentation

compare()

bool ReferenceGenome::compare	(	const std::string &	chr,
		uint32_t	pos_start,
		uint32_t	pos_end,
		const std::string &	compare_seq,
		float	match_threshold
	)		const

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getChromosomeLength()

uint32_t ReferenceGenome::getChromosomeLength

(

std::string

chr

)

const

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getChromosomes()

std::vector< std::string > ReferenceGenome::getChromosomes

(

)

const

getContigHeader()

std::string ReferenceGenome::getContigHeader

(

)

const

getFilepath()

std::string ReferenceGenome::getFilepath

(

)

const

query()

std::string_view ReferenceGenome::query	(	const std::string &	chr,
		uint32_t	pos_start,
		uint32_t	pos_end
	)		const

setFilepath()

int ReferenceGenome::setFilepath

(

std::string

fasta_filepath

)

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

• include/fasta_query.h
• src/fasta_query.cpp