Utility class to build VariantHeader objects from scratch. More...

#include <variant_header_builder.h>

Public Member Functions
	VariantHeaderBuilder () noexcept
	initializes a variant header builder More...

	VariantHeaderBuilder (const VariantHeader &header)
	initializes a variant header builder from a variant header using copy semantics More...

	VariantHeaderBuilder (const VariantHeaderBuilder &other)=delete

VariantHeaderBuilder &	operator= (const VariantHeaderBuilder &other)=delete

	VariantHeaderBuilder (VariantHeaderBuilder &&other)=default

VariantHeaderBuilder &	operator= (VariantHeaderBuilder &&other)=default

VariantHeaderBuilder &	add_chromosome (const std::string &id, const std::string &length="", const std::string &url="", const std::string &extra="")

VariantHeaderBuilder &	add_filter (const std::string &id, const std::string &description="", const std::string &extra="")

VariantHeaderBuilder &	add_shared_field (const std::string &id, const std::string &number, const std::string &type, const std::string &description="", const std::string &source="", const std::string &version="", const std::string &extra="")

VariantHeaderBuilder &	add_individual_field (const std::string &id, const std::string &number, const std::string &type, const std::string &description="", const std::string &extra="")

VariantHeaderBuilder &	add_sample (const std::string &sample)

VariantHeaderBuilder &	add_source (const std::string &source)

VariantHeaderBuilder &	advanced_add_arbitrary_line (const std::string &line)

VariantHeaderBuilder &	merge (const VariantHeader &other_header)
	merges a variant header into this builder, using bcf_hdr_combine() from htslib More...

VariantHeader	build () const
	create a new VariantHeader by copying the contents of this builder into a new object. Allows for reuse. More...

VariantHeader	one_time_build () const
	create a new VariantHeader by moving the contents of this builder into a new object. More efficient but does not allow for reuse. More...

Detailed Description

Utility class to build VariantHeader objects from scratch.

Constructor & Destructor Documentation

gamgee::VariantHeaderBuilder::VariantHeaderBuilder ( )

noexcept

initializes a variant header builder

Note: VariantReader and VariantWriter will take care of creating objects for reading and writing respectively if your goal is to write a VCF/BCF file to disk or stream.

Warning: you should only call this explicitly if you are building a VariantHeader from scratch.

gamgee::VariantHeaderBuilder::VariantHeaderBuilder ( const VariantHeader & header )

initializes a variant header builder from a variant header using copy semantics

Note: VariantReader and VariantWriter will take care of creating objects for reading and writing respectively if your goal is to write a VCF/BCF file to disk or stream.

Parameters

header the VariantHeader to use as a source for this builder

gamgee::VariantHeaderBuilder::VariantHeaderBuilder ( const VariantHeaderBuilder & other )

delete

gamgee::VariantHeaderBuilder::VariantHeaderBuilder ( VariantHeaderBuilder && other )

default

Member Function Documentation

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::add_chromosome	(	const std::string &	id,
		const std::string &	length = `""`,
		const std::string &	url = `""`,
		const std::string &	extra = `""`
	)

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::add_filter	(	const std::string &	id,
		const std::string &	description = `""`,
		const std::string &	extra = `""`
	)

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::add_individual_field	(	const std::string &	id,
		const std::string &	number,
		const std::string &	type,
		const std::string &	description = `""`,
		const std::string &	extra = `""`
	)

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::add_sample ( const std::string & sample )

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::add_shared_field	(	const std::string &	id,
		const std::string &	number,
		const std::string &	type,
		const std::string &	description = `""`,
		const std::string &	source = `""`,
		const std::string &	version = `""`,
		const std::string &	extra = `""`
	)

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::add_source ( const std::string & source )

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::advanced_add_arbitrary_line ( const std::string & line )

VariantHeader gamgee::VariantHeaderBuilder::build ( ) const

inline

create a new VariantHeader by copying the contents of this builder into a new object. Allows for reuse.

VariantHeaderBuilder & gamgee::VariantHeaderBuilder::merge ( const VariantHeader & other_header )

merges a variant header into this builder, using bcf_hdr_combine() from htslib

Parameters

header the VariantHeader to merge into this builder

VariantHeader gamgee::VariantHeaderBuilder::one_time_build ( ) const

inline

create a new VariantHeader by moving the contents of this builder into a new object. More efficient but does not allow for reuse.

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

delete

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

default

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

gamgee/variant/variant_header_builder.h
gamgee/variant/variant_header_builder.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation