cgatools::copynumber::CnvFileVcfRecordSource Class Reference

Inheritance diagram for cgatools::copynumber::CnvFileVcfRecordSource:

List of all members.

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

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Member Function Documentation

std::vector<cgatools::conv::VcfKvHeaderRecord> cgatools::copynumber::CnvFileVcfRecordSource::getKeyValueHeaderRecords

(

size_t

idxGenome

)

const [virtual]

Returns #KEY=VALUE records for the given genome.

Must include at least the source_GENOME_REFERENCE key.

Implements cgatools::conv::VcfRecordSource.

std::string cgatools::copynumber::CnvFileVcfRecordSource::getSource

(

size_t

idxGenome

)

const [virtual]

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

Implements cgatools::conv::VcfRecordSource.

std::vector<cgatools::conv::VcfSubFieldHeaderRecord> cgatools::copynumber::CnvFileVcfRecordSource::getSubFieldHeaderRecords

(

)

const [virtual]

Returns the VcfSubFieldHeaderRecords for all genomes.

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

Implements cgatools::conv::VcfRecordSource.

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

• CnvFileVcfSource.hpp