gamgee::VariantWriter Class Reference

utility class to write out a VCF/BCF file to any stream More...

#include <variant_writer.h>

Public Member Functions
	VariantWriter (const std::string &output_fname="-", const bool binary=true, const int compression_level=Z_DEFAULT_COMPRESSION)
	Creates a new VariantWriter using the specified output file name. More...
	VariantWriter (const VariantHeader &header, const std::string &output_fname="-", const bool binary=true, const int compression_level=Z_DEFAULT_COMPRESSION)
	Creates a new VariantWriter with the header extracted from a Variant record and using the specified output file name. More...
	VariantWriter (const VariantWriter &other)=delete
	a VariantWriter cannot be copied safely, as it is iterating over a stream. More...
VariantWriter &	operator= (const VariantWriter &other)=delete
	VariantWriter (VariantWriter &&other)=default
	a VariantWriter can be moved More...
VariantWriter &	operator= (VariantWriter &&other)=default
void	add_record (const Variant &body)
	Adds a record to the file stream. More...
void	add_header (const VariantHeader &header)
	Adds a header to the file stream. More...

Detailed Description

utility class to write out a VCF/BCF file to any stream

Todo:

add serialization option

Constructor & Destructor Documentation

gamgee::VariantWriter::VariantWriter ( const std::string &  output_fname = "-", const bool  binary = true, const int  compression_level = Z_DEFAULT_COMPRESSION  )

explicit

Creates a new VariantWriter using the specified output file name.

Parameters

output_fname	file to write to. The default is stdout (as defined by htslib)
binary	whether the output should be in BCF (true) or VCF format (false)
compression_level	optional zlib compression level. 0 for none, 1 for best speed, 9 for best compression

Note

the header is copied and managed internally

gamgee::VariantWriter::VariantWriter ( const VariantHeader &  header, const std::string &  output_fname = "-", const bool  binary = true, const int  compression_level = Z_DEFAULT_COMPRESSION  )

explicit

Creates a new VariantWriter with the header extracted from a Variant record and using the specified output file name.

Parameters

header	a VariantHeader object to make a copy from
output_fname	file to write to. The default is stdout (as defined by htslib)
binary	whether the output should be in BCF (true) or VCF format (false)
compression_level	optional zlib compression level. 0 for none, 1 for best speed, 9 for best compression

Note

the header is copied and managed internally

gamgee::VariantWriter::VariantWriter ( const VariantWriter &  other )

delete

a VariantWriter cannot be copied safely, as it is iterating over a stream.

gamgee::VariantWriter::VariantWriter ( VariantWriter &&  other )

default

a VariantWriter can be moved

Member Function Documentation

void gamgee::VariantWriter::add_header

(

const VariantHeader &

header

)

Adds a header to the file stream.

Parameters

header

the header

Note

the header is a requirement to add records

void gamgee::VariantWriter::add_record

(

const Variant &

body

)

Adds a record to the file stream.

Parameters

body	the record

VariantWriter& gamgee::VariantWriter::operator= ( const VariantWriter &  other )

delete

VariantWriter& gamgee::VariantWriter::operator= ( VariantWriter &&  other )

default

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

• gamgee/variant/variant_writer.h
• gamgee/variant/variant_writer.cpp