InputData Class Reference

#include <input_data.h>

Collaboration diagram for InputData:

Public Member Functions
	InputData ()
std::string	getBAMFilepath ()
void	setBAMFilepath (std::string filepath)
void	setRefGenome (std::string fasta_filepath)
FASTAQuery	getRefGenome ()
std::string	getSequence (std::string chr, int pos_start, int pos_end)
std::string	getOutputDir ()
void	setOutputDir (std::string dirpath)
std::string	getRegion ()
void	setRegion (std::string region)
int	getWindowSize ()
void	setWindowSize (int window_size)
std::string	getSNPFilepath ()
void	setSNPFilepath (std::string filepath)
std::string	getRegionChr ()
int	getRegionStart ()
int	getRegionEnd ()
bool	getRegionSet ()
void	setChrCov (std::string chr_cov)
int	getChrCov (std::string chr, double &cov)
std::string	getPFBFilepath ()
void	setPFBFilepath (std::string filepath)

Private Attributes
std::string	bam_filepath = ""
std::string	ref_filepath = ""
std::string	snp_vcf_filepath = ""
std::string	pfb_filepath = ""
FASTAQuery	fasta_query
std::string	output_dir = ""
std::string	region = ""
int	window_size = 10000
std::string	region_chr = ""
int	region_start = 0
int	region_end = 0
bool	region_set = false
std::map< std::string, double >	chr_cov

Constructor & Destructor Documentation

InputData()

InputData::InputData

(

)

Member Function Documentation

getBAMFilepath()

std::string InputData::getBAMFilepath

(

)

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getChrCov()

int InputData::getChrCov	(	std::string	chr,
		double &	cov
	)

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getOutputDir()

std::string InputData::getOutputDir

(

)

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getPFBFilepath()

std::string InputData::getPFBFilepath

(

)

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getRefGenome()

FASTAQuery InputData::getRefGenome

(

)

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getRegion()

std::string InputData::getRegion

(

)

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getRegionChr()

std::string InputData::getRegionChr

(

)

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getRegionEnd()

int InputData::getRegionEnd

(

)

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getRegionSet()

bool InputData::getRegionSet

(

)

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getRegionStart()

int InputData::getRegionStart

(

)

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getSequence()

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

getSNPFilepath()

std::string InputData::getSNPFilepath

(

)

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getWindowSize()

int InputData::getWindowSize

(

)

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setBAMFilepath()

void InputData::setBAMFilepath

(

std::string

filepath

)

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setChrCov()

void InputData::setChrCov

(

std::string

chr_cov

)

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setOutputDir()

void InputData::setOutputDir

(

std::string

dirpath

)

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setPFBFilepath()

void InputData::setPFBFilepath

(

std::string

filepath

)

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setRefGenome()

void InputData::setRefGenome

(

std::string

fasta_filepath

)

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setRegion()

void InputData::setRegion

(

std::string

region

)

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setSNPFilepath()

void InputData::setSNPFilepath

(

std::string

filepath

)

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setWindowSize()

void InputData::setWindowSize

(

int

window_size

)

Member Data Documentation

bam_filepath

std::string InputData::bam_filepath = ""

private

chr_cov

std::map<std::string, double> InputData::chr_cov

private

fasta_query

FASTAQuery InputData::fasta_query

private

output_dir

std::string InputData::output_dir = ""

private

pfb_filepath

std::string InputData::pfb_filepath = ""

private

ref_filepath

std::string InputData::ref_filepath = ""

private

region

std::string InputData::region = ""

private

region_chr

std::string InputData::region_chr = ""

private

region_end

int InputData::region_end = 0

private

region_set

bool InputData::region_set = false

private

region_start

int InputData::region_start = 0

private

snp_vcf_filepath

std::string InputData::snp_vcf_filepath = ""

private

window_size

int InputData::window_size = 10000

private

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

• include/input_data.h
• src/input_data.cpp