vcfpp::BcfWriter Class Reference

Stream out variants to compressed/uncompressed VCF/BCF file or stdout. More...

#include <vcfpp.h>

Public Member Functions
	BcfWriter ()
	Construct an empty BcfWriter.
	BcfWriter (const std::string &fname, std::string version="VCF4.1")
	Open VCF/BCF file for writing. The format is infered from file's suffix. More...
	BcfWriter (const std::string &fname, const BcfHeader &h)
	Open VCF/BCF file for writing. The format is infered from file's suffix. More...
	BcfWriter (const std::string &fname, const std::string &version, const std::string &mode)
	Open VCF/BCF file for writing using given mode. More...
	BcfWriter (const std::string &fname, const BcfHeader &h, const std::string &mode)
	Open VCF/BCF file for writing using given mode. More...
void	open (const std::string &fname)
	Open VCF/BCF file for writing. The format is infered from file's suffix. More...
void	open (const std::string &fname, const std::string &mode)
	Open VCF/BCF file for writing using given mode. More...
void	close ()
	close the BcfWriter object.
void	initalHeader (std::string version="VCF4.1")
	initial a VCF header using the internal template given a specific version. VCF4.1 is the default
void	initalHeader (const BcfHeader &h)
	initial a VCF header by pointing to header of another VCF
void	copyHeader (const std::string &vcffile, std::string samples="-")
	copy header of given VCF and restrict on samples. if samples=="", FORMAT removed and only sites left
void	writeLine (const std::string &vcfline)
	copy a string to a vcf line
bool	writeHeader ()
	streams out the header
bool	writeRecord (BcfRecord &v)
	streams out the given variant of BcfRecord type

Public Attributes
BcfHeader	header
	header object initialized by initalHeader

Detailed Description

Stream out variants to compressed/uncompressed VCF/BCF file or stdout.

Constructor & Destructor Documentation

BcfWriter() [1/4]

vcfpp::BcfWriter::BcfWriter ( const std::string &  fname, std::string  version = "VCF4.1"  )

inline

Open VCF/BCF file for writing. The format is infered from file's suffix.

Parameters

fname	The file name or "-" for stdin/stdout. For indexed files
version	The output header is constructed with the internal template given a specific version

BcfWriter() [2/4]

vcfpp::BcfWriter::BcfWriter ( const std::string &  fname, const BcfHeader &  h  )

inline

Open VCF/BCF file for writing. The format is infered from file's suffix.

Parameters

fname	The file name or "-" for stdin/stdout. For indexed files
h	The output header is pointing to the given BcfHeader object

BcfWriter() [3/4]

vcfpp::BcfWriter::BcfWriter ( const std::string &  fname, const std::string &  version, const std::string &  mode  )

inline

Open VCF/BCF file for writing using given mode.

Parameters

fname	The file name or "-" for stdin/stdout. For indexed files
version	The output header is constructed with the internal template given a specific version
mode	Mode matching [w]b .. compressed BCF [w]bu .. uncompressed BCF [w]z .. compressed VCF [w] .. uncompressed VCF

BcfWriter() [4/4]

vcfpp::BcfWriter::BcfWriter ( const std::string &  fname, const BcfHeader &  h, const std::string &  mode  )

inline

Open VCF/BCF file for writing using given mode.

Parameters

fname	The file name or "-" for stdin/stdout. For indexed files
h	The output header is pointing to the given BcfHeader object
mode	Mode matching [w]b .. compressed BCF [w]bu .. uncompressed BCF [w]z .. compressed VCF [w] .. uncompressed VCF

Member Function Documentation

open() [1/2]

void vcfpp::BcfWriter::open ( const std::string &  fname )

inline

Open VCF/BCF file for writing. The format is infered from file's suffix.

Parameters

fname

The file name or "-" for stdin/stdout. For indexed files

open() [2/2]

void vcfpp::BcfWriter::open ( const std::string &  fname, const std::string &  mode  )

inline

Open VCF/BCF file for writing using given mode.

Parameters

fname	The file name or "-" for stdin/stdout. For indexed files
mode	Mode matching [w]b .. compressed BCF [w]bu .. uncompressed BCF [w]z .. compressed VCF [w] .. uncompressed VCF

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

• vcfpp.h