BED file base class. More...

#include <varfiles.hpp>

Inheritance diagram for sampFiles::BedFile:

Collaboration diagram for sampFiles::BedFile:

Public Member Functions
	BedFile ()
	Default constructor.

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

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

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

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

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

	~BedFile ()
	Destructor.

virtual void	open ()
	Open stream (does nothing)

void	close ()
	Close stream.

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

	GbinFile (const string &fileName, const size_t &nCols, const size_t &elemSize)
	Constructor with file name. More...

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

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

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

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

	~GbinFile ()
	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 Attributes
fstream	_famFile
	Corresponding .fam file stream.

fstream	_bimFile
	Corresponding .bim file stream.

string	_fileStub
	File name stub (minus the extension)

Protected Attributes inherited from sampFiles::GbinFile
string	_fileName
	File name.

size_t	_nCols
	Number of elements in a row.

size_t	_elemSize
	Size of each element in bytes.

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

Static Protected Attributes
static const vector< char >	_masks = {static_cast<char>(0x03), static_cast<char>(0x0C), static_cast<char>(0x30), static_cast<char>(0xC0)}
	Genotype bit masks. More...

static const unordered_map< char, string >	_tests
	Genotype bit tests. More...

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

Detailed Description

BED file base class.

Sets up streams for the auxiliary files.

Constructor & Destructor Documentation

◆ BedFile()

BedFile::BedFile ( const string & stubName )

File name constructor.

Parameters

[in] stubName file name minus the extension

Member Data Documentation

◆ _masks

const vector< char > BedFile::_masks = {static_cast<char>(0x03), static_cast<char>(0x0C), static_cast<char>(0x30), static_cast<char>(0xC0)}

staticprotected

Genotype bit masks.

Used to isolate each of the four genotypes (moving from the last bit pair) from the .bed two-bit genotype coding.

◆ _tests

const unordered_map< char, string > BedFile::_tests

staticprotected

Initial value:

= {
    {'M', {static_cast<char>(0x01), static_cast<char>(0x04), static_cast<char>(0x10), static_cast<char>(0x40)}},
    {'H', {static_cast<char>(0x02), static_cast<char>(0x08), static_cast<char>(0x20), static_cast<char>(0x80)}}
}

Genotype bit tests.

Used to test each of the four genotypes (moving from the last bit pair) from the .bed two-bit genotype coding for the possible states.

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

Public Member Functions

Protected Attributes