vcfpp::BcfReader Class Reference

Stream in variants from compressed/uncompressed VCF/BCF file or stdin. More...

#include <vcfpp.h>

Public Member Functions
	BcfReader ()
	Construct an empty BcfReader.
	BcfReader (const std::string &file)
	construct a vcf/bcf reader from file. More...
	BcfReader (const std::string &file, const std::string &region)
	construct a vcf/bcf reader with subset samples More...
	BcfReader (const std::string &file, const std::string &region, const std::string &samples)
	construct a vcf/bcf reader with subset samples in target region More...
void	close ()
	close the BcfReader object.
void	open (const std::string &file)
	open a VCF/BCF/STDIN file for streaming in
int	setThreads (int n)
	set the number of threads to use
const BcfHeader &	getHeader () const
	return a BcfHeader object
uint64_t	getVariantsCount (BcfRecord &r, const std::string &region)
	get the number of records of given region
void	setSamples (const std::string &samples)
	explicitly stream to specific samples More...
void	setRegion (const std::string &region)
	explicitly stream to specific region More...
bool	getNextVariant (BcfRecord &r)
	read in the next variant More...

Public Attributes
BcfHeader	header
	a BcfHeader object
int	nsamples
	number of samples in the VCF
std::vector< std::string >	SamplesName
	number of samples in the VCF

Detailed Description

Stream in variants from compressed/uncompressed VCF/BCF file or stdin.

Constructor & Destructor Documentation

BcfReader() [1/3]

vcfpp::BcfReader::BcfReader ( const std::string &  file )

inline

construct a vcf/bcf reader from file.

Parameters

file	the input vcf/bcf with suffix vcf(.gz)/bcf(.gz) or stdin "-"

BcfReader() [2/3]

vcfpp::BcfReader::BcfReader ( const std::string &  file, const std::string &  region  )

inline

construct a vcf/bcf reader with subset samples

Parameters

file	the input vcf/bcf with suffix vcf(.gz)/bcf(.gz) or stdin "-"
region	samtools-like region "chr:start-end", skip if empty

BcfReader() [3/3]

vcfpp::BcfReader::BcfReader ( const std::string &  file, const std::string &  region, const std::string &  samples  )

inline

construct a vcf/bcf reader with subset samples in target region

Parameters

file	the input vcf/bcf with suffix vcf(.gz) or bcf(.gz)
region	samtools-like region "chr:start-end", skip if empty
samples	LIST samples to include or exclude as a comma-separated string. LIST : select samples in list ^LIST : exclude samples from list "-" : include all samples "" : exclude all samples

Member Function Documentation

getNextVariant()

bool vcfpp::BcfReader::getNextVariant ( BcfRecord &  r )

inline

read in the next variant

Parameters

r	r is a BcfRecord object to be filled in.

setRegion()

void vcfpp::BcfReader::setRegion ( const std::string &  region )

inline

explicitly stream to specific region

Parameters

region

the string is samtools-like format which is chr:start-end

setSamples()

void vcfpp::BcfReader::setSamples ( const std::string &  samples )

inline

explicitly stream to specific samples

Parameters

samples

the string is bcftools-like format, which is comma separated list of samples to include (or exclude with "^" prefix).

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

• vcfpp.h