HMP file input class. More...

#include <varfiles.hpp>

Inheritance diagram for sampFiles::HmpFileI:

Collaboration diagram for sampFiles::HmpFileI:

Public Member Functions
	HmpFileI ()
	Default constructor.

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

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

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

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

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

	~HmpFileI ()
	Destructor.

void	open ()
	Open stream to read.

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

uint64_t	nsnp ()
	Number of SNPs in the object.

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

Detailed Description

HMP file input class.

Reads HMP files, skipping or copying the header as necessary.

Constructor & Destructor Documentation

◆ HmpFileI()

HmpFileI::HmpFileI ( const string & fileName )

File name constructor.

Parameters

[in] fileName file name including extension

Member Function Documentation

◆ _numLines()

uint64_t HmpFileI::_numLines ( )

protected

Get number of SNPs in the HMP file.

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

Returns: number of SNPs

◆ sample()

void HmpFileI::sample	(	HmpFileO &	out,
		const uint64_t &	n
	)

Sample SNPs and save to HMP 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.