BED file input class. More...

#include <varfiles.hpp>

Inheritance diagram for sampFiles::BedFileI:

Collaboration diagram for sampFiles::BedFileI:

Public Member Functions
	BedFileI ()
	Default constructor.

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

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

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

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

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

	~BedFileI ()
	Destructor.

void	open ()
	Open stream to read.

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

void	sampleLD (const uint64_t &n)
	Linkage disequilibrium among sampled sites. More...

void	sampleLD (const PopIndex &popID, const uint64_t &n)
	LD among sampled sites within populations. 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::BedFile
	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.

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 Member Functions
uint64_t	_numLines ()
	Get number of lines in the `_bimFile` More...

uint64_t	_famLines ()
	Get number of lines in the `_famFile` More...

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

void	_ld (const char snp1, const char snp2, const size_t &N, const unsigned short &pad, double &rSq, double &Dprime, double &dcnt1, double &dcnt2)
	Between-SNP linkage disequilibrium (LD) More...

void	_ld (const char snp1, const char snp2, const PopIndex &popID, vector< double > &rSq, vector< double > &Dprime, vector< double > &dcnt1, vector< double > &dcnt2)
	Between-SNP LD within populations. More...

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

Additional Inherited Members
Protected Attributes inherited from sampFiles::BedFile
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 inherited from sampFiles::BedFile
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...

Detailed Description

BED file input class.

Reads BED files and the auxiliary files that come with them (.fam and .bim) as necessary. Only the SNP-major version is supported.

Constructor & Destructor Documentation

◆ BedFileI()

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

inline

File name constructor.

Parameters

[in] stubName file name minus the extension

Member Function Documentation

◆ _famLines() [1/2]

uint64_t BedFileI::_famLines ( )

protected

Get number of lines in the _famFile

Assumes Unix-like line endings. The result is equal to the number of individuals.

Returns: number of lines in _famFile

◆ _famLines() [2/2]

uint64_t BedFileI::_famLines ( fstream & fam )

protected

Copy the .fam file and count number of lines.

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

Parameters

[in] fam .fam file stream

Returns: number of lines in _famFile

◆ _ld() [1/2]

void BedFileI::_ld	(	const char *	snp1,
		const char *	snp2,
		const PopIndex &	popID,
		vector< double > &	rSq,
		vector< double > &	Dprime,
		vector< double > &	dcnt1,
		vector< double > &	dcnt2
	)

protected

Between-SNP LD within populations.

Calculates two LD statistics ( \( r^2 \) and \( D' \)) between two SNPs from a BED file. Missing values are ignored. If there are fewer than three haplotypes with data present at both loci, the return values are -9. This value is also returned if one of the loci is monomorphic after taking out missing data at the other SNP. Minor (not necessarily derived) allele counts are also reported to enable downstream filtering. Note that the populations are assumed diploid and the counts are of haploid chromosomes (i.e. one homozygote yields count of 2). The values are calculted within each population as indicated by the PopIndex object. The results are returned in the supplied vectors, which are assumed to be of correct size. Since this is an internal function unexposed to the user, this is not chaecked to save on compuation steps. Care must be taken that the char arrays passed to the function have lengths compatible with the number of individuals indexed by PopIndex. This is not checked.

Parameters

[in]	snp1	first SNP
[in]	snp2	second SNP
[in]	popID	population index
[out]	rSq	vector of \( r^2 \) estimates
[out]	Dprime	vector of \( D' \) estimates
[out]	dcnt1	vector of minor allele counts at locus 1
[out]	dcnt2	vector of minor allele counts at locus 2

◆ _ld() [2/2]

void BedFileI::_ld	(	const char *	snp1,
		const char *	snp2,
		const size_t &	N,
		const unsigned short &	pad,
		double &	rSq,
		double &	Dprime,
		double &	dcnt1,
		double &	dcnt2
	)

protected

Between-SNP linkage disequilibrium (LD)

Calculates two LD statistics ( \( r^2 \) and \( D' \)) between two SNPs from a BED file. Missing values are ignored. If there are fewer than three haplotypes with data present at both loci, the return values are -9. This value is also returned if one of the loci is monomorphic after taking out missing data at the other SNP. Minor (not necessarily derived) allele counts are also reported to enable downstream filtering. Note that the populations are assumed diploid and the counts are of haploid chromosomes (i.e. one homozygote yields count of 2).

Parameters

[in]	snp1	first SNP
[in]	snp2	second SNP
[in]	N	length of the genotype vector in bytes (four genotypes per byte)
[in]	pad	number of bit pairs of padding in the last byte
[out]	rSq	the \( r^2 \) estimate
[out]	Dprime	the \( D' \) estimate
[out]	dcnt1	minor allele count at locus 1
[out]	dcnt2	minor allele count at locus 2

◆ _numLines()

uint64_t BedFileI::_numLines ( )

protected

Get number of lines in the _bimFile

Assumes Unix-like line endings. The result is equal to the number of SNPs.

Returns: number of lines in _bimFile

◆ sample()

void BedFileI::sample	(	BedFileO &	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

◆ sampleLD() [1/2]

void BedFileI::sampleLD	(	const PopIndex &	popID,
		const uint64_t &	n
	)

LD among sampled sites within populations.

Samples sequential pairs of SNPs and calculates two LD measures ( \( r^2 \) and \( D' \)) within populations indicated by PopIndex. Saves to a file with the same name as the one preceding the .bed etc extensions, but adds _LD.tsv at the end. Each line is tab-delimited with the chromosome number (from the .bim file), between-SNP distance, non-reference allele count for each SNP, \( r^2 \), and \( D' \). Missing data are ignored (only pairwise-complete observations are included). If one of the SNPs is monomorphic or if the total number of pairwise present genotypes is fewer than three (exclusive), the LD measures are returned as -9 to indicate missing values.

Parameters

[in]	popID	population index
[in]	n	number of SNP pairs to sample

◆ sampleLD() [2/2]

void BedFileI::sampleLD ( const uint64_t & n )

Linkage disequilibrium among sampled sites.

Samples sequential pairs of SNPs and calculates two LD measures ( \( r^2 \) and \( D' \)). Saves to a file with the same name as the one preceding the .bed etc extensions, but adds _LD.tsv at the end. Each line is tab-delimited with the chromosome number (from the .bim file), between-SNP distance, non-reference allele count for each SNP, \( r^2 \), and \( D' \). Missing data are ignored (only pairwise-complete observations are included). If one of the SNPs is monomorphic or if the total number of pairwise present genotypes is fewer than three (exclusive), the LD measures are returned as -9 to indicate missing values.

Parameters

[in] n number of SNP pairs 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

◆ BedFileI()

Member Function Documentation

◆ _famLines() [1/2]

◆ _famLines() [2/2]

◆ _ld() [1/2]

◆ _ld() [2/2]

◆ _numLines()

◆ sample()

◆ sampleLD() [1/2]

◆ sampleLD() [2/2]