cgatools::cgdata::EvidenceReader::IntervalRecord Struct Reference

Public Member Functions
reference::Range	getRange () const
bool	isCompatible (uint16_t alleleIndex, const variants::Call &call, const reference::CrrFile &crr) const
	Returns true if the given call is compatible to the evidence allele at the specified index.
bool	isCompatible (uint16_t alleleIndex, const reference::Range &range, const std::string &seq, bool ignoreAdjacentInsertions) const
	Returns true if the sequence is compatible to the evidence allele at the specified index.
std::string	getAlignment (size_t alleleIndex) const
Static Public Member Functions
static void	bindToParser (util::DelimitedFile &parser, IntervalRecord &rec, const reference::CrrFile &crr)
static std::string	cigarToAlignment (const std::string &cigar)
Public Attributes
int32_t	intervalId_
uint16_t	chromosome_
uint32_t	offset_
uint32_t	length_
uint16_t	ploidy_
int32_t	score_
std::vector< uint16_t >	alleleIndexes_
boost::array< std::string, 3 >	alleles_
boost::array< std::string, 2 >	alleleAlignments_

Member Function Documentation

bool cgatools::cgdata::EvidenceReader::IntervalRecord::isCompatible	(	uint16_t	alleleIndex,
		const reference::Range &	range,
		const std::string &	seq,
		bool	ignoreAdjacentInsertions
	)			const

Returns true if the sequence is compatible to the evidence allele at the specified index.

ignoreAdjacentInsertions controls whether the comparison to the allele includes or skips the inserted sequence at the boundaries of the given range.

bool cgatools::cgdata::EvidenceReader::IntervalRecord::isCompatible	(	uint16_t	alleleIndex,
		const variants::Call &	call,
		const reference::CrrFile &	crr
	)			const

Returns true if the given call is compatible to the evidence allele at the specified index.

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