cgatools::mapping::GapEst::GapsEstimator Class Reference

Estimates wobble (small) gap probabilities, based on the sequence at a particular offset from the end of the clone. More...

Public Types
typedef cgdata::SmallGapTuple	GapTuple
typedef SequenceRetriever::Sequence	Sequence
Public Member Functions
	GapsEstimator (const ArmData &armData, size_t side, boost::uint32_t seed)
void	loadGaps (const std::string &gapFile0, const std::string &gapFile1)
	Load gaps according to the spec.
double	getProbability (GapTuple gaps, const SequenceRetriever &sr) const
	Get P(gaps\|sequence), where sequence is retrieved using sr.
double	getProbability (GapTuple gaps) const
	Get P(gaps) where the sequence is unknown.
void	getGapTuples (double fraction, std::vector< GapTuple > &result) const
	Returns as few gap pairs as possible to cover at least the specified fraction of hDNB population.
GapTuple	randomGaps (const SequenceRetriever &sr) const
	Get a random GapTuple, according to P(gaps\|sequence), where sequence is retrieved using sr.
size_t	gapCount () const
	The number of wobble (small) gaps described by this GapsEstimator.

Detailed Description

Estimates wobble (small) gap probabilities, based on the sequence at a particular offset from the end of the clone.

void cgatools::mapping::GapEst::GapsEstimator::getGapTuples	(	double	fraction,
		std::vector< GapTuple > &	result
	)			const

Returns as few gap pairs as possible to cover at least the specified fraction of hDNB population.

GapTuple cgatools::mapping::GapEst::GapsEstimator::randomGaps ( const SequenceRetriever & sr ) const

Get a random GapTuple, according to P(gaps|sequence), where sequence is retrieved using sr.

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