#include <yat/omic/VcfFile.h>

Inheritance diagram for theplu::yat::omic::VcfFile:

Public Member Functions
	VcfFile (void)
	default constructor

	VcfFile (const std::string &fn)

void	close (void)
	close file

bool	good (void) const

bool	is_open (void) const

void	open (const std::string &fn)
	open file named fn More...

bool	read (VCF &vcf)

VcfHeader &	header (void)

const VcfHeader &	header (void) const

Friends
class	VcfIterator

Detailed Description

Since: New in yat 0.16

Constructor & Destructor Documentation

◆ VcfFile()

theplu::yat::omic::VcfFile::VcfFile ( const std::string & fn )

explicit

Opens file named fn.

See also: open

Member Function Documentation

◆ good()

bool theplu::yat::omic::VcfFile::good ( void ) const

A file is good when it's open and until reading an entry failed.

Returns: true if file is still good

◆ header() [1/2]

VcfHeader& theplu::yat::omic::VcfFile::header ( void )

Returns: reference to header

Note that modifying the referenced object does not modify the underlying file.

Note: If file is not open, behaviour is undefined.

◆ header() [2/2]

const VcfHeader& theplu::yat::omic::VcfFile::header ( void ) const

Returns: reference to header

Note: If file is not open, behaviour is undefined.

◆ is_open()

bool theplu::yat::omic::VcfFile::is_open ( void ) const

Returns: true if file is open

◆ open()

void theplu::yat::omic::VcfFile::open ( const std::string & fn )

open file named fn

Open file fn, unless fn is "-", in which case stdin is used. The function tries to detect whether file is compressed (gzipped) or not by looking at the first byte which is 0x1f for gzipped files.

Function opens a VcfHeader and if the first bit does not conform with the format of a VCF header, an excpetion is thrown.

Note: If file already is open behaviour is undefined.

◆ read()

bool theplu::yat::omic::VcfFile::read ( VCF & vcf )

Read one VCF entry from file and assign to vcf. If there is no more entry to read, the state of the file is switched to bad and false is returned.

Returns: true if successful

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

yat/omic/VcfFile.h

Public Member Functions

Friends