VCF file input class. More...

#include <varfiles.hpp>

Inheritance diagram for sampFiles::VcfFileI:

Collaboration diagram for sampFiles::VcfFileI:

Public Member Functions
	VcfFileI ()
	Default constructor.

	VcfFileI (const string &fileName)
	File name constructor. More...

	VcfFileI (const VcfFileI &in)=default
	Copy constructor.

VcfFileI &	operator= (const VcfFileI &in)=default
	Copy assignment.

	VcfFileI (VcfFileI &&in)=default
	Move constructor.

VcfFileI &	operator= (VcfFileI &&in)=default
	Move assignment.

	~VcfFileI ()
	Destructor.

void	open ()
	Open stream to read.

void	sample (VcfFileO &out, const uint64_t &n)
	Sample SNPs and save to VCF file. More...

uint64_t	nsnp ()
	Number of SNPs in the object.

Public Member Functions inherited from sampFiles::VcfFile
	VcfFile ()
	Default constructor.

	VcfFile (const string &fileName)
	Constructor with file name. More...

	VcfFile (const VcfFile &in)=default
	Copy constructor.

VcfFile &	operator= (const VcfFile &in)=default
	Copy assignment.

	VcfFile (VcfFile &&in)=default
	Move constructor.

VcfFile &	operator= (VcfFile &&in)=default
	Move assignment.

	~VcfFile ()
	Destructor.

void	close ()
	Close stream.

Public Member Functions inherited from sampFiles::GtxtFile
	GtxtFile ()
	Default constructor.

	GtxtFile (const string &fileName)
	Constructor with file name. More...

	GtxtFile (const string &fileName, const bool &head)
	Constructor with file name and header indicator. More...

	GtxtFile (const GtxtFile &in)=default
	Copy constructor.

GtxtFile &	operator= (const GtxtFile &in)=default
	Copy assignment.

	GtxtFile (GtxtFile &&in)=default
	Move constructor.

GtxtFile &	operator= (GtxtFile &&in)=default
	Move assignment.

	~GtxtFile ()
	Destructor.

Public Member Functions inherited from sampFiles::VarFile
	VarFile (const VarFile &in)=default
	Copy constructor.

VarFile &	operator= (const VarFile &in)=default
	Copy assignment.

	VarFile (VarFile &&in)=default
	Move constructor.

VarFile &	operator= (VarFile &&in)=default
	Move assignment.

	~VarFile ()
	Destructor.

Protected Member Functions
uint64_t	_numLines ()
	Get number of SNPs in the VCF file. More...

Protected Member Functions inherited from sampFiles::VarFile
	VarFile ()
	Default constructor (protected)

Additional Inherited Members
Protected Attributes inherited from sampFiles::GtxtFile
string	_fileName
	File name.

bool	_head
	Is there a header?

Protected Attributes inherited from sampFiles::VarFile
fstream	_varFile
	Variant file stream.

Detailed Description

VCF file input class.

Reads VCF files, skipping or copying the header as necessary; .idx files are ignored.

Constructor & Destructor Documentation

◆ VcfFileI()

sampFiles::VcfFileI::VcfFileI ( const string & fileName )

inline

File name constructor.

Parameters

[in] fileName file name including extension

Member Function Documentation

◆ _numLines()

uint64_t VcfFileI::_numLines ( )

protected

Get number of SNPs in the VCF file.

Assumes Unix-like line endings. Header is not counted.

Returns: number of SNPs

◆ sample()

void VcfFileI::sample	(	VcfFileO &	out,
		const uint64_t &	n
	)

Sample SNPs and save to VCF file.

Sample \(n\) SNPs without replacement from the file represented by the current object and save to the out object. Uses Vitter's [3] method. Number of samples has to be smaller that the number of SNPs in the file.

Parameters

[in]	out	output object
[in]	n	number of SNPs to sample

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

Public Member Functions