Extends reference_site_info to include genotype data and allele counts. More...

#include <variant.hpp>

Inheritance diagram for reference_variant:

Collaboration diagram for reference_variant:

Public Member Functions
	reference_variant ()

	reference_variant (const std::string &_chrom, std::uint32_t _pos, const std::string &_id, const std::string &_ref, const std::string &_alt, float _err, float _recom, double _cm, std::size_t _ac, std::vector< std::int8_t > _gt)

Public Member Functions inherited from reference_site_info
	reference_site_info ()

	reference_site_info (std::string _chrom, std::uint32_t _pos, std::string _id, std::string _ref, std::string _alt, float _err, float _recom, double _cm)

Public Attributes
std::size_t	ac = 0
	Allele count.

std::vector< std::int8_t >	gt
	Genotype vector.

Public Attributes inherited from reference_site_info
std::string	chrom
	Chromosome name.

std::uint32_t	pos = 0
	Position on the chromosome.

std::string	id
	Variant identifier.

std::string	ref
	Reference allele.

std::string	alt
	Alternate allele.

float	err = std::numeric_limits<float>::quiet_NaN()
	Error rate.

float	recom = std::numeric_limits<float>::quiet_NaN()
	Recombination rate.

double	cm = std::numeric_limits<double>::quiet_NaN()
	Centimorgan position.

Detailed Description

Extends reference_site_info to include genotype data and allele counts.

Constructor & Destructor Documentation

reference_variant::reference_variant ( )

inline

reference_variant::reference_variant	(	const std::string &	_chrom,
		std::uint32_t	_pos,
		const std::string &	_id,
		const std::string &	_ref,
		const std::string &	_alt,
		float	_err,
		float	_recom,
		double	_cm,
		std::size_t	_ac,
		std::vector< std::int8_t >	_gt )