cgatools::junctions::JunctionVcfRecordWriter Class Reference

Inheritance diagram for cgatools::junctions::JunctionVcfRecordWriter:

Public Member Functions
cgatools::reference::Location	getLocation () const
	Get 0-based location of first base of VCF record.
void	writeId (std::ostream &out) const
	Write ID field of VCF record.
void	writeRef (std::ostream &out) const
	Write REF field of VCF record.
void	writeAlt (std::ostream &out) const
	Write ALT field of VCF record.
void	writeQual (std::ostream &out) const
	Write QUAL field of VCF record.
void	writeFilter (std::ostream &out) const
	Write FILTER field of VCF record.
void	writeInfo (std::ostream &out) const
	Write INFO field of VCF record.
void	writeFormat (std::ostream &out) const
	Write FORMAT field of VCF record.
void	writeSample (std::ostream &out, size_t gIdx) const
	Write per-sample field of VCF record, for the given genome.
Protected Attributes
cgatools::reference::Location	pos_
std::vector< std::string >	sample_
std::string	id_
std::string	ref_
std::string	alt_
std::string	qual_
std::string	filter_
std::string	info_
std::string	format_
Friends
class	JunctionVcfRecordSource

Member Function Documentation

cgatools::reference::Location cgatools::junctions::JunctionVcfRecordWriter::getLocation ( ) const [virtual]

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

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

void cgatools::junctions::JunctionVcfRecordWriter::writeSample	(	std::ostream &	out,
		size_t	idxGenome
	)			const `[virtual]`

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

Genomes are numbered starting with 0 for the first genome.

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