#include <yat/omic/VcfHeader.h>

Public Member Functions
	VcfHeader (const std::string &version)
	Constructor. More...

	VcfHeader (std::istream &is)

void	add (const std::string &key, const std::string &value)

void	add (const std::string &key, const std::string &ID, int number, const std::string &type, const std::string &description)

void	add_info (const std::string &ID, const std::string &number, const std::string &type, const std::string &description)

void	add_format (const std::string &ID, const std::string &number, const std::string &type, const std::string &description)

void	add_program_command (int argc, char *argv[])

void	add_program_version (const std::string &prog, const std::string &version)

void	erase (size_t line)
	erase line line More...

const std::string &	header (void) const

void	header (const std::string &header)

const std::string &	line (size_t i) const

std::string	key (size_t line) const

void	nicify (void)

std::string	value (size_t line) const

std::string	value (size_t line, const std::string &key) const

size_t	size (void) const

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

void	samples (const std::vector< std::string > &s)

Friends
std::ostream &	operator<< (std::ostream &os, const VcfHeader &b)

Related Functions
(Note that these are not member functions.)
std::ostream &	operator<< (std::ostream &, const VcfHeader &header)

Detailed Description

Since: New in yat 0.16

Constructor & Destructor Documentation

◆ VcfHeader() [1/2]

theplu::yat::omic::VcfHeader::VcfHeader ( const std::string & version )

Constructor.

Creates an empty header

◆ VcfHeader() [2/2]

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

Consumes lines until a line does not start with '#' and constructs a VcfHeader.

Member Function Documentation

◆ add() [1/2]

void theplu::yat::omic::VcfHeader::add	(	const std::string &	key,
		const std::string &	value
	)

Adds a line ##key = value

◆ add() [2/2]

void theplu::yat::omic::VcfHeader::add	(	const std::string &	key,
		const std::string &	ID,
		int	number,
		const std::string &	type,
		const std::string &	description
	)

Add a line

key=<ID,Number=number,Type=type,Description=description>

If number is 0, it's replaced with ".".

◆ add_format()

void theplu::yat::omic::VcfHeader::add_format	(	const std::string &	ID,
		const std::string &	number,
		const std::string &	type,
		const std::string &	description
	)

Same as add("FORMAT", ID, number, type, description)

number should be integer or special character as A: one per alt allele R: one per allele G: one per genotype .: unknown

◆ add_info()

void theplu::yat::omic::VcfHeader::add_info	(	const std::string &	ID,
		const std::string &	number,
		const std::string &	type,
		const std::string &	description
	)

Same as add("INFO", ID, number, type, description)

number should be integer or special character as A: one per alt allele R: one per allele G: one per genotype .: unknown

◆ add_program_command()

void theplu::yat::omic::VcfHeader::add_program_command	(	int	argc,
		char *	argv[]
	)

add a line with something like:

bcftools_viewCommand=view -l 9 -O z -; Date=Wed Apr 19 10:49:09 2017

◆ add_program_version()

void theplu::yat::omic::VcfHeader::add_program_version	(	const std::string &	prog,
		const std::string &	version
	)

add a line with something like

bcftools_normVersion=1.4+htslib-1.4

◆ erase()

void theplu::yat::omic::VcfHeader::erase ( size_t line )

erase line line

The last line, starting with '#CHROM', cannot be erased. Use function samples(const std::vector<std::string>&) to alter that line.

Since: New in yat 0.18

◆ header() [1/2]

const std::string& theplu::yat::omic::VcfHeader::header ( void ) const

Returns: the last line of the header

◆ header() [2/2]

void theplu::yat::omic::VcfHeader::header ( const std::string & header )

Set the last line of the header

◆ key()

std::string theplu::yat::omic::VcfHeader::key ( size_t line ) const

Returns: everything between prefix '##' and first '=' of line line

◆ line()

const std::string& theplu::yat::omic::VcfHeader::line ( size_t i ) const

Returns: line i

◆ nicify()

void theplu::yat::omic::VcfHeader::nicify ( void )

Sort lines

Lines are sorted with respect to their categories a) '##fileformat=' b) '##reference=' and '##contig=' c) '##INFO=' d) '##FILTER=' e) '##FORMAT=' f) other g) '#CHROM'

◆ samples() [1/2]

const std::vector<std::string>& theplu::yat::omic::VcfHeader::samples ( void ) const

Sample names occur tab-delimited in the last line starting from 10th column.

Returns: samples name

◆ samples() [2/2]

void theplu::yat::omic::VcfHeader::samples ( const std::vector< std::string > & s )

Set sample names

◆ size()

size_t theplu::yat::omic::VcfHeader::size ( void ) const

Returns: number of lines

◆ value() [1/2]

std::string theplu::yat::omic::VcfHeader::value ( size_t line ) const

everything right of first '=' on line line

◆ value() [2/2]

std::string theplu::yat::omic::VcfHeader::value	(	size_t	line,
		const std::string &	key
	)		const

returns "" if key is missing is false otherwise corresponding value e.g. value(i, "Description") returns value for key Description of line line

Friends And Related Function Documentation

◆ operator<<()

std::ostream & operator<<	(	std::ostream &	,
		const VcfHeader &	header
	)

Since: new in yat 0.16

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

yat/omic/VcfHeader.h

Public Member Functions

Friends

Related Functions