varfiles.hpp File Reference

Read and write genetic variant files. More...

#include <fstream>
#include <string>
#include <vector>
#include <unordered_map>
#include <cstdint>
#include <limits>
#include "populations.hpp"

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Classes
class	sampFiles::VarFile
	Base variant file class. More...
class	sampFiles::GbinFile
	Generic binary file base class. More...
class	sampFiles::GbinFileI
	Binary file input class. More...
class	sampFiles::GbinFileO
	Generic binary file output class. More...
class	sampFiles::BedFile
	BED file base class. More...
class	sampFiles::BedFileI
	BED file input class. More...
class	sampFiles::BedFileO
	BED file output class. More...
class	sampFiles::GtxtFile
	Generic text file base class. More...
class	sampFiles::GtxtFileI
	Text file input class. More...
class	sampFiles::GtxtFileO
	Generic text file output class. More...
class	sampFiles::TpedFile
	TPED file base class. More...
class	sampFiles::TpedFileI
	TPED file input class. More...
class	sampFiles::TpedFileO
	TPED file output class. More...
class	sampFiles::VcfFile
	VCF file base class. More...
class	sampFiles::VcfFileI
	VCF file input class. More...
class	sampFiles::VcfFileO
	VCF file output class. More...
class	sampFiles::HmpFile
	Hapmap (HMP) file base class. More...
class	sampFiles::HmpFileI
	HMP file input class. More...
class	sampFiles::HmpFileO
	HMP file output class. More...

Variables
static const size_t	sampFiles::BUF_SIZE = 10485760
	Buffer size. More...
const double	sampFiles::EPS = numeric_limits<double>::epsilon()
	Machine \(\epsilon\).
const double	sampFiles::PI = 3.14159265358979323846264338328
	pi

Detailed Description

Read and write genetic variant files.

Author

Anthony J. Greenberg

Copyright

Copyright (c) 2017 Anthony J. Greenberg

Version

0.1

Definitions and interface documentation for classes that read and write various genetic variant file formats.

Currently supported formats:

• plink BED
• plink TPED
• VCF
• Hapmap (.hmp.txt)

Variable Documentation

BUF_SIZE

const size_t sampFiles::BUF_SIZE = 10485760

static

Buffer size.

Size of the buffer for reading files text files. I use it in functions that count the number of lines, for example. The buffer size (10M) is optimized for a MacBook Pro with an SSD. Other systems may perform better with a different value (e.g., if you have a spinning drive and more RAM you may want to experiemtn with increasing it).