TPED file input class. More...

#include <varfiles.hpp>

Inheritance diagram for sampFiles::TpedFileI:

Collaboration diagram for sampFiles::TpedFileI:

Public Member Functions
	TpedFileI ()
	Default constructor.

	TpedFileI (const string &stubName)
	File name constructor. More...

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

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

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

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

	~TpedFileI ()
	Destructor.

void	open ()
	Open stream to read.

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

uint64_t	nsnp ()
	Number of SNPs in the object.

uint64_t	nindiv ()
	Number of individuals in the object.

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

	TpedFile (const string &stubName)
	File name constructor. More...

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

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

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

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

	~TpedFile ()
	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	_famLines ()
	Get number of lines in the `_tfamFile` More...

uint64_t	_famLines (fstream &fam)
	Copy the .tfam file and count number of lines. More...

void	_famCopy (fstream &fam)
	Copy the .tfam file. More...

uint64_t	_numLines ()
	Get number of rows in the text file. More...

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

Additional Inherited Members
Protected Attributes inherited from sampFiles::TpedFile
fstream	_tfamFile
	Corresponding .tfam file stream.

string	_fileStub
	File name stub (minus the extension)

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

TPED file input class.

Reads TPED files and the corresponding .tfam files as necessary.

Constructor & Destructor Documentation

◆ TpedFileI()

sampFiles::TpedFileI::TpedFileI ( const string & stubName )

inline

File name constructor.

Parameters

[in] stubName file name minus the extension

Member Function Documentation

◆ _famCopy()

void TpedFileI::_famCopy ( fstream & fam )

protected

Copy the .tfam file.

The current object's .tfam file is copied to the provided file stream, which should already be open for writing. If not, the function throws a string object `‘Output .fam filestream not open’'.

Parameters

[in] fam .tfam file stream

◆ _famLines() [1/2]

uint64_t TpedFileI::_famLines ( )

protected

Get number of lines in the _tfamFile

Assumes Unix-like line endings. The result is equal to the number of individuals. The _tfamFile should already be open for reading.

Returns: number of lines in _tfamFile

◆ _famLines() [2/2]

uint64_t TpedFileI::_famLines ( fstream & fam )

protected

Copy the .tfam file and count number of lines.

Assumes Unix-like line endings. The result is equal to the number of individuals. The current object's .tfam file is copied to the provided file stream, which should already be open for writing. If not, the function throws a string object `‘Output .fam filestream not open’'.

Parameters

[in] fam .tfam file stream

Returns: number of lines in _tfamFile

◆ _numLines()

uint64_t TpedFileI::_numLines ( )

protected

Get number of rows in the text file.

Assumes Unix-like line endings. Header, if present, is not counted. Is overriden in some, but not all, derived classes.

Returns: number of rows

◆ sample()

void TpedFileI::sample	(	TpedFileO &	out,
		const uint64_t &	n
	)

Sample SNPs and save to BED 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

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TpedFileI()

Member Function Documentation

◆ _famCopy()

◆ _famLines() [1/2]

◆ _famLines() [2/2]

◆ _numLines()

◆ sample()