Object represents a variant record in the VCF, offering methods to access and modify fields. More...

#include <vcfpp.h>

Public Member Functions
	BcfRecord ()
	empty constructor. call init() afterwards

	BcfRecord (BcfHeader &h)
	constructor with a given BcfHeader object

void	initHeader (BcfHeader &h)
	initilize the header associated with BcfRecord object by pointing to another BcfHeader object

void	resetHeader (BcfHeader &h)
	reset the header associated with BcfRecord object by pointing to another BcfHeader object

std::string	asString () const
	return current variant as raw string

template<typename T >
isValidGT< T >	getGenotypes (T &v)
	fill in the input vector with genotypes of 0 and 1. only works for ploidy<=2. Genotypes with missing allele is coded as heterozygous More...

bool	getGenotypes (std::vector< int > &v)
	fill in the input vector with genotype values, 0, 1 or -9 (missing). More...

template<typename T , typename S = typename T::value_type>
isFormatVector< T >	getFORMAT (std::string tag, T &v)
	get tag value in FORMAT More...

bool	getFORMAT (std::string tag, std::vector< std::string > &v)
	get tag value in FORMAT More...

template<typename T , typename S = typename T::value_type>
isInfoVector< T >	getINFO (std::string tag, T &v)
	get tag value in INFO More...

template<typename T >
isScalar< T >	getINFO (std::string tag, T &v)
	get tag value in INFO More...

template<typename T >
isString< T >	getINFO (std::string tag, T &v)
	get tag value in INFO More...

template<typename T >
isScalar< T >	setINFO (std::string tag, const T &v)
	set tag value for INFO More...

template<typename T >
isValidInfo< T >	setINFO (std::string tag, const T &v)
	set tag value for INFO More...

void	removeINFO (std::string tag)
	remove the given tag from INFO of the variant

bool	setGenotypes (const std::vector< int > &v)
	set genotypes from scratch even if genotypes not present More...

void	setPhasing (const std::vector< char > &v)
	set phasing status for all diploid samples using given vector More...

void	removeFORMAT (std::string tag)
	remove the given tag from FORMAT of the variant

template<typename T >
isValidFMT< T >	setFORMAT (std::string tag, const T &v)
	set tag values for all samples in FORMAT using given vector More...

template<typename T >
isScalar< T >	setFORMAT (std::string tag, const T &v)
	set tag for a single sample in FORMAT using given singular value. this works only when there is one sample in the vcf More...

void	addLineFromString (const std::string &vcfline)
	add one variant record from given string

bool	isNoneMissing () const
	if all samples have non missing values for the tag in FORMAT

bool	isSV () const
	return boolean value indicates if current variant is Structual Variant or not

bool	isIndel () const
	return boolean value indicates if current variant is exclusively INDEL

bool	isMultiAllelics () const
	return boolean value indicates if current variant is multiallelic sites

bool	isMultiAllelicSNP () const
	return boolean value indicates if current variant is exclusively multiallelic SNP sites

bool	isSNP () const
	return boolean value indicates if current variant is exclusively biallelic SNP. Note ALT=* are skipped

bool	hasSNP () const
	return boolean value indicates if current variant has SNP type defined in vcf.h (htslib>=1.16)

bool	hasINDEL () const
	return boolean value indicates if current variant has INDEL type defined in vcf.h (htslib>=1.16)

bool	hasINS () const
	return boolean value indicates if current variant has INS type defined in vcf.h (htslib>=1.16)

bool	hasDEL () const
	return boolean value indicates if current variant has DEL type defined in vcf.h (htslib>=1.16)

bool	hasMNP () const
	return boolean value indicates if current variant has MNP type defined in vcf.h (htslib>=1.16)

bool	hasBND () const
	return boolean value indicates if current variant has BND type defined in vcf.h (htslib>=1.16)

bool	hasOTHER () const
	return boolean value indicates if current variant has OTHER type defined in vcf.h (htslib>=1.16)

bool	hasOVERLAP () const
	return boolean value indicates if current variant has OVERLAP type defined in vcf.h (htslib>=1.16)

std::string	CHROM () const
	return CHROM name

std::string	ID () const
	return ID field

int64_t	POS () const
	return 1-base position

void	setCHR (const std::string &s)
	modify CHROM value

void	setPOS (int64_t p)
	modify position given 1-based value

void	setID (const std::string &s)
	update ID

void	setRefAlt (const std::string &s)
	set REF and ALT alleles given a string seperated by comma

void	setQUAL (float q)
	modify the QUAL value

void	setQUAL (char q)
	modify the QUAL value

void	setFILTER (const std::string &s)
	modify the FILTER value

int64_t	Start () const
	return 0-base start of the variant (can be any type)

int64_t	End () const
	return 0-base end of the variant (can be any type)

std::string	REF () const
	return raw REF alleles as string

void	swap_REF_ALT ()
	swap REF and ALT for biallelic SNP

std::string	ALT () const
	return raw ALT alleles as string

float	QUAL ()
	return QUAL value

std::string	FILTER ()
	return raw FILTER column as string

std::string	allINFO ()
	return raw INFO column as string. recommend to use getINFO for specific tag.

bool	allPhased () const
	return boolean value indicates if genotypes of all samples are phased

int	ploidy () const
	return the number of ploidy of current variant

void	setPloidy (int v)
	in a rare case, one may want to set the number of ploidy manually

Public Attributes
std::vector< char >	isGenoMissing
	if there is "." in GT for the sample, then it's coded as missing (TRUE)

std::vector< char >	typeOfGT
	vector of nsamples length. keep track of the type of genotype (one of GT_HOM_RR, GT_HET_RA, GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). More...

std::vector< char >	gtPhase
	vector of nsamples length. keep track of the phasing status of each sample

Friends
class	BcfReader

class	BcfWriter

std::ostream &	operator<< (std::ostream &out, const BcfRecord &v)
	stream out the variant

Detailed Description

Object represents a variant record in the VCF, offering methods to access and modify fields.

Note: BcfRecord has to be associated with a BcfHeader object and needs to be filled in by calling BcfReader.getNextVariant function.

Member Function Documentation

◆ getFORMAT() [1/2]

bool vcfpp::BcfRecord::getFORMAT	(	std::string	tag,
		std::vector< std::string > &	v
	)

inline

get tag value in FORMAT

Parameters

tag	valid tag name in FORMAT column declared in the VCF header
v	vector of string

Returns: bool

◆ getFORMAT() [2/2]

template<typename T , typename S = typename T::value_type>

isFormatVector<T> vcfpp::BcfRecord::getFORMAT	(	std::string	tag,
		T &	v
	)

inline

get tag value in FORMAT

Parameters

tag	valid tag name in FORMAT column declared in the VCF header
v	valid input include vector of float, char, int type

Returns: bool

◆ getGenotypes() [1/2]

bool vcfpp::BcfRecord::getGenotypes ( std::vector< int > & v )

inline

fill in the input vector with genotype values, 0, 1 or -9 (missing).

Parameters

v	valid input is vector<int> type

Returns: bool

Note: this function provides full capability to handle all kinds of genotypes in multi-ploidy data costing more spae than the other function. missing allele is set as -9.

◆ getGenotypes() [2/2]

template<typename T >

isValidGT<T> vcfpp::BcfRecord::getGenotypes ( T & v )

inline

fill in the input vector with genotypes of 0 and 1. only works for ploidy<=2. Genotypes with missing allele is coded as heterozygous

Parameters

v	valid input includes vector<bool> and vector<char> type

Returns: bool

Note: use isNoneMissing() to check if all genotypes are with no missingness. Alternatively, one can use vector<int> as the input type as noted in the other overloading function getGenotypes().

◆ getINFO() [1/3]

template<typename T , typename S = typename T::value_type>

isInfoVector<T> vcfpp::BcfRecord::getINFO	(	std::string	tag,
		T &	v
	)

inline

get tag value in INFO

Parameters

tag	valid tag name in INFO column declared in the VCF header
v	valid input include vector of float, int type

Returns: bool

◆ getINFO() [2/3]

template<typename T >

isScalar<T> vcfpp::BcfRecord::getINFO	(	std::string	tag,
		T &	v
	)

inline

get tag value in INFO

Parameters

tag	valid tag name in INFO column declared in the VCF header
v	valid input include scalar value of float or int type

Returns: bool

◆ getINFO() [3/3]

template<typename T >

isString<T> vcfpp::BcfRecord::getINFO	(	std::string	tag,
		T &	v
	)

inline

get tag value in INFO

Parameters

tag	valid tag name in INFO column declared in the VCF header
v	valid input is std::string

Returns: bool

◆ setFORMAT() [1/2]

template<typename T >

isValidFMT<T> vcfpp::BcfRecord::setFORMAT	(	std::string	tag,
		const T &	v
	)

inline

set tag values for all samples in FORMAT using given vector

Parameters

tag	valid tag name in FORMAT column declared in the VCF header
v	valid input include vector<int>, vector<float>, vector<char>, std::string

Returns: bool

◆ setFORMAT() [2/2]

template<typename T >

isScalar<T> vcfpp::BcfRecord::setFORMAT	(	std::string	tag,
		const T &	v
	)

inline

set tag for a single sample in FORMAT using given singular value. this works only when there is one sample in the vcf

Parameters

tag	valid tag name in FORMAT column declared in the VCF header
v	valid input include int, float or double

Returns: void

◆ setGenotypes()

bool vcfpp::BcfRecord::setGenotypes ( const std::vector< int > & v )

inline

set genotypes from scratch even if genotypes not present

Parameters

v	the genotypes of vector<int> type

Returns: bool

◆ setINFO() [1/2]

template<typename T >

isScalar<T> vcfpp::BcfRecord::setINFO	(	std::string	tag,
		const T &	v
	)

inline

set tag value for INFO

Parameters

tag	valid tag name in INFO column declared in the VCF header
v	valid input include scalar value of float or int type

Returns: bool

◆ setINFO() [2/2]

template<typename T >

isValidInfo<T> vcfpp::BcfRecord::setINFO	(	std::string	tag,
		const T &	v
	)

inline

set tag value for INFO

Parameters

tag	valid tag name in INFO column declared in the VCF header
v	valid input include vector<int> vector<float> std::string

Returns: bool

◆ setPhasing()

void vcfpp::BcfRecord::setPhasing ( const std::vector< char > & v )

inline

set phasing status for all diploid samples using given vector

Parameters

v	valid input includes vector<char>

Member Data Documentation

◆ typeOfGT

std::vector<char> vcfpp::BcfRecord::typeOfGT

vector of nsamples length. keep track of the type of genotype (one of GT_HOM_RR, GT_HET_RA, GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN).

Note: GT_HOM_RR 0
GT_HOM_AA 1
GT_HET_RA 2
GT_HET_AA 3
GT_HAPL_R 4
GT_HAPL_A 5
GT_UNKN 6

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

vcfpp.h

Public Member Functions

Public Attributes

Friends

Detailed Description

Member Function Documentation

◆ getFORMAT() [1/2]

◆ getFORMAT() [2/2]

◆ getGenotypes() [1/2]

◆ getGenotypes() [2/2]

◆ getINFO() [1/3]

◆ getINFO() [2/3]

◆ getINFO() [3/3]

◆ setFORMAT() [1/2]

◆ setFORMAT() [2/2]

◆ setGenotypes()

◆ setINFO() [1/2]

◆ setINFO() [2/2]

◆ setPhasing()

Member Data Documentation

◆ typeOfGT