#include <yat/omic/VCF.h>

Classes
class	Data
	class holiding data stored in FORMAT and data fields More...

class	Info
	class handling the INFO field in an VCF entry More...

Public Member Functions
	VCF (void)
	default constructor

	VCF (size_t n)

	VCF (const std::string &)
	Construct entry from a std::string.

	VCF (std::istream &is)

void	chromosome (const std::string &chr)
	set chromosome name

const std::string &	chromosome (void) const

void	pos (int32_t p)
	set position

const int32_t &	pos (void) const

void	id (const std::string &id)
	Variant identifier. More...

const std::string &	id (void) const

void	ref (const std::string &r)
	set refererence sequence at position involved in variant

void	ref (char r)
	set refererence sequence at position involved in variant

const std::string &	ref (void) const

void	alt (const std::string &a)
	set alternative sequence(s) More...

void	alt (char a)
	set alternative sequence(s) More...

const std::string &	alt (void) const

const std::vector< std::string > &	alts (void) const

void	alts (const std::vector< std::string > &a)
	set alternative alleles

void	alts (std::vector< std::string > &&a)
	set alternative alleles

unsigned int	n_alleles (void) const

const std::string &	qual (void) const
	phred-scaled probability that all samples are wildtype

void	qual (const std::string &q)
	set quality

void	qual (unsigned int q)
	set quality

const std::string &	filter (void) const

const std::vector< std::string > &	filters (void) const

void	add_filter (const std::string &)
	append list of filters

void	filter (const std::string &)
	set filters

void	subset (const std::vector< size_t > &index)

VCF::Info &	info (void)
	set info

const VCF::Info &	info (void) const

const Data &	data (void) const
	access data

Data &	data (void)
	access data

unsigned int	n_samples (void) const

void	n_samples (int n)
	set number of samples to n

Friends
std::ostream &	operator<< (std::ostream &, const VCF &)

Related Functions
(Note that these are not member functions.)
std::ostream &	operator<< (std::ostream &os, const VCF &vcf)
	output operator for VCF More...

std::istream &	operator>> (std::istream &is, VCF &vcf)
	input operator for VCF More...

Detailed Description

Class to parse and modify an entry in a VcfFile (Variant Call Format) as defined in https://samtools.github.io/hts-specs/VCFv4.2.pdf

Since: new in yat 0.16

Constructor & Destructor Documentation

◆ VCF() [1/2]

theplu::yat::omic::VCF::VCF ( size_t n )

explicit

Create a VCF representing n samples.

Since: New in yat 0.20

◆ VCF() [2/2]

theplu::yat::omic::VCF::VCF ( std::istream & is )

explicit

Equivalent with

std::string line;
std::getline(is, line);
VCF(line);

Member Function Documentation

◆ alt() [1/3]

void theplu::yat::omic::VCF::alt ( const std::string & a )

set alternative sequence(s)

Parameters

a	is a comma-delimited list of sequences

◆ alt() [2/3]

void theplu::yat::omic::VCF::alt ( char a )

set alternative sequence(s)

Parameters

a	is a comma-delimited list of sequences

◆ alt() [3/3]

const std::string& theplu::yat::omic::VCF::alt ( void ) const

Returns: alternative sequence(s)

◆ alts()

const std::vector<std::string>& theplu::yat::omic::VCF::alts ( void ) const

Returns: alternative sequences

◆ chromosome()

const std::string& theplu::yat::omic::VCF::chromosome ( void ) const

Returns: Chromosome name

◆ filter()

const std::string& theplu::yat::omic::VCF::filter ( void ) const

Returns: semicolon delimited list of filters that the variant fails

◆ filters()

const std::vector<std::string>& theplu::yat::omic::VCF::filters ( void ) const

Returns: filters

◆ id() [1/2]

void theplu::yat::omic::VCF::id ( const std::string & id )

Variant identifier.

Usually the dbSNP rsID

◆ id() [2/2]

const std::string& theplu::yat::omic::VCF::id ( void ) const

Returns: Variant identifier

◆ info()

const VCF::Info& theplu::yat::omic::VCF::info ( void ) const

Returns: container holiding information in INFO field (column 8)

◆ n_alleles()

unsigned int theplu::yat::omic::VCF::n_alleles ( void ) const

Returns: number of alternative sequences

◆ n_samples()

unsigned int theplu::yat::omic::VCF::n_samples ( void ) const

Returns: number of samples

◆ pos()

const int32_t& theplu::yat::omic::VCF::pos ( void ) const

Returns: position

◆ ref()

const std::string& theplu::yat::omic::VCF::ref ( void ) const

Returns: reference sequence at position

◆ subset()

void theplu::yat::omic::VCF::subset ( const std::vector< size_t > & index )

Create a VCF with subset of samples in other defined by index.

If present, INFO fields AC and AN are recalculated to match the subset.

See also: VCF::Data.subset(const std::vector<size_t>&)

Since: New in yat 0.20

Friends And Related Function Documentation

◆ operator<<()

std::ostream & operator<<	(	std::ostream &	os,
		const VCF &	vcf
	)

Returns: stream

◆ operator>>()

std::istream & operator>>	(	std::istream &	is,
		VCF &	vcf
	)

If is is good and next character is not EOF, a VCF is read into vcf as if it was created with the istream constructor.

Returns: stream

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

yat/omic/VCF.h

Classes

Public Member Functions

Friends

Related Functions