cgatools::conv::VcfRecordWriter Class Reference

Abstract base class that writes a VCF record. More...

#include <VcfRecordSource.hpp>

Inheritance diagram for cgatools::conv::VcfRecordWriter:

List of all members.

Public Member Functions
void	writeRecord (std::ostream &out, const cgatools::reference::CrrFile &crr, size_t sampleCount) const
	Write the VCF record to out.
virtual cgatools::reference::Location	getLocation () const =0
	Get 0-based location of first base of VCF record.
virtual void	writeId (std::ostream &out) const
	Write ID field of VCF record.
virtual void	writeRef (std::ostream &out) const =0
	Write REF field of VCF record.
virtual void	writeAlt (std::ostream &out) const =0
	Write ALT field of VCF record.
virtual void	writeQual (std::ostream &out) const
	Write QUAL field of VCF record.
virtual void	writeFilter (std::ostream &out) const
	Write FILTER field of VCF record.
virtual void	writeInfo (std::ostream &out) const =0
	Write INFO field of VCF record.
virtual void	writeFormat (std::ostream &out) const =0
	Write FORMAT field of VCF record.
virtual void	writeSample (std::ostream &out, size_t idxGenome) const =0
	Write per-sample field of VCF record, for the given genome.
Static Public Member Functions
static std::string	getVcfChromosomeName (size_t chromosomeId, const cgatools::reference::CrrFile &crr)
	Get the chromosome name for the given chromosome ID, as written in a VCF record.

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Detailed Description

Abstract base class that writes a VCF record.

Classes derived from this include SmallVariantsVcfRecordWriter, etc.

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Member Function Documentation

virtual cgatools::reference::Location cgatools::conv::VcfRecordWriter::getLocation

(

)

const [pure virtual]

Get 0-based location of first base of VCF record.

The value output to the VCF file is at Location.offset+1.

Implemented in cgatools::copynumber::CnvFileVcfRecordWriter, cgatools::junctions::JunctionVcfRecordWriter, cgatools::mobileelement::MeiFileVcfRecordWriter, and cgatools::variants::VariantFileVcfRecordWriter.

static std::string cgatools::conv::VcfRecordWriter::getVcfChromosomeName	(	size_t	chromosomeId,
		const cgatools::reference::CrrFile &	crr
	)			[static]

Get the chromosome name for the given chromosome ID, as written in a VCF record.

I.e. no "chr" prefix.

void cgatools::conv::VcfRecordWriter::writeRecord	(	std::ostream &	out,
		const cgatools::reference::CrrFile &	crr,
		size_t	sampleCount
	)			const

Write the VCF record to out.

Not overridable in sub-classes, but this just calls all the per-column write() functions, which are overridable in sub-classes.

virtual void cgatools::conv::VcfRecordWriter::writeSample	(	std::ostream &	out,
		size_t	idxGenome
	)			const [pure virtual]

Write per-sample field of VCF record, for the given genome.

Genomes are numbered starting with 0 for the first genome.

Implemented in cgatools::copynumber::CnvFileVcfRecordWriter, cgatools::junctions::JunctionVcfRecordWriter, cgatools::mobileelement::MeiFileVcfRecordWriter, and cgatools::variants::VariantFileVcfRecordWriter.

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

• VcfRecordSource.hpp