cgatools::conv::VcfRecordSource Class Reference

Abstract base class that provides a stream of VcfRecordWriter. More...

#include <VcfRecordSource.hpp>

Inheritance diagram for cgatools::conv::VcfRecordSource:

List of all members.

Public Member Functions
virtual std::vector < VcfSubFieldHeaderRecord >	getSubFieldHeaderRecords () const =0
	Returns the VcfSubFieldHeaderRecords for all genomes.
virtual std::string	getSource (size_t idxGenome) const =0
	Returns the #source=VALUE header value for the given genome, which is the same as the input file's getMetadata().getSoftwareVersionString().
virtual std::vector < VcfKvHeaderRecord >	getKeyValueHeaderRecords (size_t idxGenome) const =0
	Returns #KEY=VALUE records for the given genome.
virtual std::string	getAssemblyId (size_t idxGenome) const =0
	Returns the input file's getMetadata().get("ASSEMBLY_ID").
virtual bool	eof () const =0
	Record iteration.
virtual VcfRecordSource &	operator++ ()=0
virtual const VcfRecordWriter &	operator* () const =0
virtual const VcfRecordWriter *	operator-> () const =0

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Detailed Description

Abstract base class that provides a stream of VcfRecordWriter.

Classes derived from this include SmallVariantsVcfRecordSource, etc.

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Member Function Documentation

virtual std::vector<VcfKvHeaderRecord> cgatools::conv::VcfRecordSource::getKeyValueHeaderRecords

(

size_t

idxGenome

)

const [pure virtual]

Returns #KEY=VALUE records for the given genome.

Must include at least the source_GENOME_REFERENCE key.

Implemented in cgatools::copynumber::CnvFileVcfRecordSource, cgatools::junctions::JunctionVcfRecordSource, cgatools::mobileelement::MeiFileVcfRecordSource, and cgatools::variants::VariantFileVcfRecordSource.

virtual std::string cgatools::conv::VcfRecordSource::getSource

(

size_t

idxGenome

)

const [pure virtual]

Returns the #source=VALUE header value for the given genome, which is the same as the input file's getMetadata().getSoftwareVersionString().

Implemented in cgatools::copynumber::CnvFileVcfRecordSource, cgatools::junctions::JunctionVcfRecordSource, cgatools::mobileelement::MeiFileVcfRecordSource, and cgatools::variants::VariantFileVcfRecordSource.

virtual std::vector<VcfSubFieldHeaderRecord> cgatools::conv::VcfRecordSource::getSubFieldHeaderRecords

(

)

const [pure virtual]

Returns the VcfSubFieldHeaderRecords for all genomes.

Includes, INFO, FORMAT, FILTER, and ALT records.

Implemented in cgatools::copynumber::CnvFileVcfRecordSource, cgatools::junctions::JunctionVcfRecordSource, cgatools::mobileelement::MeiFileVcfRecordSource, and cgatools::variants::VariantFileVcfRecordSource.

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

• VcfRecordSource.hpp