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 VCF file and its associated files.
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
int	getStatus (const std::string &region)
	query the status of a given region in the VCF More...
int	getVariantsCount (const std::string &region)
	count the number of variants by iterating through a given region. More...
void	setSamples (const std::string &samples)
	explicitly stream to specific samples More...
void	setRegion (const std::string &region)
	explicitly stream to specific region. throw invalid_argument error if index file not found. throw runtime_error if the region was not a valid bcftools-like format or was not presenting in the VCF. 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
	a vector of samples name 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	the BcfRecord object to be filled in.

getStatus()

int vcfpp::BcfReader::getStatus ( const std::string &  region )

inline

query the status of a given region in the VCF

Returns

-2: the region is not a valid bcftools-like format, or it is not presenting in the VCF even though it's bcftols-like format.
-1: there is no index file found.
0: the region is valid but empty.
1: vaild and not empty.

getVariantsCount()

int vcfpp::BcfReader::getVariantsCount ( const std::string &  region )

inline

count the number of variants by iterating through a given region.

Note

If you want to continue work on that region, remember to reset the region by setRegion()!
Also, check the status of the region first to handle the different cases!

setRegion()

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

inline

explicitly stream to specific region. throw invalid_argument error if index file not found. throw runtime_error if the region was not a valid bcftools-like format or was not presenting in the VCF.

Parameters

region

the string for region is samtools-like format, which can be 'chr', 'chr:start' and '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