cgatools::variants::PhasedAllele Class Reference

Class to hold allele-specific information for a PhasedHypothesis. More...

Public Member Functions
	PhasedAllele ()
	Creates an empty PhasedAllele.
void	addCall (const Call &call, const reference::CrrFile &crr)
	Adds the given call to the PhasedAllele.
void	addSequence (const Call &call, const std::string &sequence)
	Adds the given call to the allele sequence, overriding the sequence for the call.
bool	hasHapLink (const std::string &hapLink) const
	Returns true if any call in this PhasedAllele has the hapLink.
const std::string &	allele () const
	Returns the full sequence of this PhasedAllele.
const std::vector< uint32_t > &	pos () const
	Returns the list of positions in allele_ of each call in calls_, plus allele_.size().
const std::vector< const Call * > &	calls () const
	Returns the list of calls comprising this PhasedAllele.

Detailed Description

Class to hold allele-specific information for a PhasedHypothesis.

void cgatools::variants::PhasedAllele::addSequence	(	const Call &	call,
		const std::string &	sequence
	)

Adds the given call to the allele sequence, overriding the sequence for the call.

This is used for no-call and ref calls whenever the locus ends in the middle of the no-call or ref call.

const std::vector<uint32_t>& cgatools::variants::PhasedAllele::pos ( ) const [inline]

Returns the list of positions in allele_ of each call in calls_, plus allele_.size().

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