cgatools::mapping::GapAndConcordanceExtractor Class Reference

The class scans a given alignment for a given allele, provided by AlleleSequenceAligner in the constructor. More...

#include <AlleleAlignment.hpp>

Inheritance diagram for cgatools::mapping::GapAndConcordanceExtractor:

List of all members.

Public Member Functions
	GapAndConcordanceExtractor (const AlleleSequenceAligner &alleleAligner)
void	run (uint8_t side, bool strand, int32_t offsetInAllele, const std::string &alignmentCigar, const std::string &readSequence, const std::string &readScores)
Public Attributes
std::vector< int8_t >	gaps_
double	concordance_
int32_t	endOffsetInAllele_
size_t	mismatches_
Protected Attributes
const AlleleSequenceAligner &	alleleAligner_
size_t	halfDnbSize_

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Detailed Description

The class scans a given alignment for a given allele, provided by AlleleSequenceAligner in the constructor.

While scanning it detects the gaps and computes the product of probabilities of bases (concordance), the number of mismatches and end position of the alignment

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

• AlleleAlignment.hpp