CNVCaller Class Reference

#include <cnv_caller.h>

Collaboration diagram for CNVCaller:

Public Member Functions
	CNVCaller (std::shared_mutex &shared_mutex)
Genotype	getGenotypeFromCNState (int cn_state) const
std::tuple< double, SVType, Genotype, int >	runCopyNumberPrediction (std::string chr, const CHMM &hmm, uint32_t start_pos, uint32_t end_pos, double mean_chr_cov, const std::vector< uint32_t > &pos_depth_map, const InputData &input_data) const
void	runCIGARCopyNumberPrediction (std::string chr, std::vector< SVCall > &sv_candidates, const CHMM &hmm, double mean_chr_cov, const std::vector< uint32_t > &pos_depth_map, const InputData &input_data) const
void	calculateMeanChromosomeCoverage (const std::vector< std::string > &chromosomes, std::unordered_map< std::string, std::vector< uint32_t > > &chr_pos_depth_map, std::unordered_map< std::string, double > &chr_mean_cov_map, const std::string &bam_filepath, int thread_count) const
void	readSNPAlleleFrequencies (std::string chr, uint32_t start_pos, uint32_t end_pos, std::vector< uint32_t > &snp_pos, std::unordered_map< uint32_t, double > &snp_baf, std::unordered_map< uint32_t, double > &snp_pfb, const InputData &input_data) const
void	saveSVCopyNumberToTSV (SNPData &snp_data, std::string filepath, std::string chr, uint32_t start, uint32_t end, std::string sv_type, double likelihood) const
void	saveSVCopyNumberToJSON (SNPData &before_sv, SNPData &after_sv, SNPData &snp_data, std::string chr, uint32_t start, uint32_t end, std::string sv_type, double likelihood, const std::string &filepath) const

Public Attributes
const std::unordered_map< int, Genotype >	StateGenotypeMap

Constructor & Destructor Documentation

CNVCaller()

CNVCaller::CNVCaller ( std::shared_mutex &  shared_mutex )

inline

Member Function Documentation

calculateMeanChromosomeCoverage()

void CNVCaller::calculateMeanChromosomeCoverage	(	const std::vector< std::string > &	chromosomes,
		std::unordered_map< std::string, std::vector< uint32_t > > &	chr_pos_depth_map,
		std::unordered_map< std::string, double > &	chr_mean_cov_map,
		const std::string &	bam_filepath,
		int	thread_count
	)		const

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getGenotypeFromCNState()

Genotype CNVCaller::getGenotypeFromCNState ( int  cn_state ) const

inline

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readSNPAlleleFrequencies()

void CNVCaller::readSNPAlleleFrequencies	(	std::string	chr,
		uint32_t	start_pos,
		uint32_t	end_pos,
		std::vector< uint32_t > &	snp_pos,
		std::unordered_map< uint32_t, double > &	snp_baf,
		std::unordered_map< uint32_t, double > &	snp_pfb,
		const InputData &	input_data
	)		const

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runCIGARCopyNumberPrediction()

void CNVCaller::runCIGARCopyNumberPrediction	(	std::string	chr,
		std::vector< SVCall > &	sv_candidates,
		const CHMM &	hmm,
		double	mean_chr_cov,
		const std::vector< uint32_t > &	pos_depth_map,
		const InputData &	input_data
	)		const

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runCopyNumberPrediction()

std::tuple< double, SVType, Genotype, int > CNVCaller::runCopyNumberPrediction	(	std::string	chr,
		const CHMM &	hmm,
		uint32_t	start_pos,
		uint32_t	end_pos,
		double	mean_chr_cov,
		const std::vector< uint32_t > &	pos_depth_map,
		const InputData &	input_data
	)		const

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saveSVCopyNumberToJSON()

void CNVCaller::saveSVCopyNumberToJSON	(	SNPData &	before_sv,
		SNPData &	after_sv,
		SNPData &	snp_data,
		std::string	chr,
		uint32_t	start,
		uint32_t	end,
		std::string	sv_type,
		double	likelihood,
		const std::string &	filepath
	)		const

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saveSVCopyNumberToTSV()

void CNVCaller::saveSVCopyNumberToTSV	(	SNPData &	snp_data,
		std::string	filepath,
		std::string	chr,
		uint32_t	start,
		uint32_t	end,
		std::string	sv_type,
		double	likelihood
	)		const

Member Data Documentation

StateGenotypeMap

const std::unordered_map<int, Genotype> CNVCaller::StateGenotypeMap

Initial value:

= {
            {0, Genotype::UNKNOWN},
            {1, Genotype::HOMOZYGOUS_ALT},
            {2, Genotype::HETEROZYGOUS},
            {3, Genotype::HOMOZYGOUS_REF},
            {4, Genotype::HOMOZYGOUS_ALT},
            {5, Genotype::HETEROZYGOUS},
            {6, Genotype::HOMOZYGOUS_ALT}
        }

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

• include/cnv_caller.h
• src/cnv_caller.cpp