theplu::yat::omic::VcfHeader Class Reference

#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)
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

theplu::yat::omic::VcfHeader::VcfHeader

(

const std::string &

version

)

Constructor.

Creates an empty header

theplu::yat::omic::VcfHeader::VcfHeader

(

std::istream &

is

)

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

Member Function Documentation

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

Adds a line ##key = value

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 ".".

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)

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

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

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

const std::string& theplu::yat::omic::VcfHeader::header

(

void

)

const

Returns

the last line of the header

void theplu::yat::omic::VcfHeader::header

(

const std::string &

header

)

Set the last line of the header

std::string theplu::yat::omic::VcfHeader::key

(

size_t

line

)

const

Returns

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

const std::string& theplu::yat::omic::VcfHeader::line

(

size_t

i

)

const

Returns

line i

void theplu::yat::omic::VcfHeader::nicify

(

void

)

Sort lines

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

void theplu::yat::omic::VcfHeader::samples

(

const std::vector< std::string > &

s

)

Set sample names

size_t theplu::yat::omic::VcfHeader::size

(

void

)

const

Returns

number of lines

std::string theplu::yat::omic::VcfHeader::value

(

size_t

line

)

const

everything right of first '=' on line line

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

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

related

Since

new in yat 0.16

---

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

• yat/omic/VcfHeader.h