cgatools::mapping::GapProbabilityAndConcordanceExtractor Class Reference

The class extends GapAndConcordanceExtractor by computing the probablility of sequence-dependent gaps in addition to the metrics computed by the parent class. More...

#include <AlleleAlignment.hpp>

Inheritance diagram for cgatools::mapping::GapProbabilityAndConcordanceExtractor:

List of all members.

Public Member Functions
	GapProbabilityAndConcordanceExtractor (const AlleleSequenceAligner &alleleAligner, boost::array< boost::shared_ptr< GapEst::GapsEstimator >, 2 > gapsEstimators)
	takes an allele aligned and a sequence-dependant gap estimator
void	run (uint8_t side, bool strand, int32_t offsetInAllele, const std::string &alignmentCigar, const std::string &readSequence, const std::string &readScores)
Public Attributes
double	gapProbability_
Protected Attributes
boost::array < boost::shared_ptr < GapEst::GapsEstimator >, 2 >	gapsEstimators_

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Detailed Description

The class extends GapAndConcordanceExtractor by computing the probablility of sequence-dependent gaps in addition to the metrics computed by the parent class.

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

• AlleleAlignment.hpp