vcfpp::BcfHeader Class Reference

Object represents header of the VCF, offering methods to access and modify the tags. More...

#include <vcfpp.h>

Public Member Functions
	BcfHeader (std::string version)
	initial a VCF header using the internal template given a specific version.
	BcfHeader (const bcf_hdr_t *h)
	make a copy from existing header
bcf_hdr_t *	get () const
	Return the raw bcf_hdr_t.
void	addINFO (const std::string &id, const std::string &number, const std::string &type, const std::string &description)
	add INFO field to header More...
void	addFORMAT (const std::string &id, const std::string &number, const std::string &type, const std::string &description)
	add FORMAT field to header More...
void	addFILTER (const std::string &id, const std::string &description)
	add one FILTER line to header More...
void	addContig (const std::string &id)
	add contig to header More...
void	addLine (const std::string &str)
	add one line to header
void	addSample (const std::string &sample) const
	add one sample name to header
std::string	asString () const
	return header as a string
std::vector< std::string >	getSamples () const
	return all samples in a string vector
std::vector< std::string >	getSeqnames () const
	return all contig/chromosome names in a string vector
int	getFormatType (std::string tag) const
	get the type of a given tag More...
int	getInfoType (std::string tag) const
	get the type of a given tag More...
void	removeContig (std::string tag) const
	remove a contig tag from header
void	removeInfo (std::string tag) const
	remove a INFO tag from header
void	removeFormat (std::string tag) const
	remove a FORMAT tag from header
void	removeFilter (std::string tag) const
	remove a FILTER tag from header
void	updateSamples (const std::string &samples)
	update the sample id in the header More...
void	setSamples (const std::string &samples) const
	explicitly set samples to be extracted More...
void	setVersion (const std::string &version) const
	set the VCF version
int	nSamples () const
	return the number of samples in the VCF

Friends
class	BcfRecord
class	BcfReader
class	BcfWriter
std::ostream &	operator<< (std::ostream &out, const BcfHeader &h)
	stream out the header

Detailed Description

Object represents header of the VCF, offering methods to access and modify the tags.

Note

BcfHeader has 3 friends, BcfReader, BcfWriter and BcfRecord.

Member Function Documentation

addContig()

void vcfpp::BcfHeader::addContig ( const std::string &  id )

inline

add contig to header

Parameters

id	contig or chromosome name

addFILTER()

void vcfpp::BcfHeader::addFILTER ( const std::string &  id, const std::string &  description  )

inline

add one FILTER line to header

Parameters

id	FILTER name
description	Description of the FILTER

addFORMAT()

void vcfpp::BcfHeader::addFORMAT ( const std::string &  id, const std::string &  number, const std::string &  type, const std::string &  description  )

inline

add FORMAT field to header

Parameters

id	tag name in FORMAT field
number	Number of elements
type	Integer, Floast or String
description	Description of the tag

addINFO()

void vcfpp::BcfHeader::addINFO ( const std::string &  id, const std::string &  number, const std::string &  type, const std::string &  description  )

inline

add INFO field to header

Parameters

id	tag name in INFO field
number	Number of elements
type	Integer, Floast or String
description	Description of the tag

getFormatType()

int vcfpp::BcfHeader::getFormatType ( std::string  tag ) const

inline

get the type of a given tag

Parameters

tag	in the FORMAT

Returns

1: int; 2: float; 3: string; 0: error;

getInfoType()

int vcfpp::BcfHeader::getInfoType ( std::string  tag ) const

inline

get the type of a given tag

Parameters

tag	in the INFO

Returns

1: int; 2: float; 3: string; 0: error; -1: no such tag in INFO

setSamples()

void vcfpp::BcfHeader::setSamples ( const std::string &  samples ) const

inline

explicitly set samples to be extracted

Parameters

samples

samples to include or exclude as a comma-separated string

updateSamples()

void vcfpp::BcfHeader::updateSamples ( const std::string &  samples )

inline

update the sample id in the header

Parameters

samples

a comma-separated string for multiple new samples

Note

this only update the samples name in a given sequential order

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

• vcfpp.h