AlleleAlignment.hpp File Reference

#include "cgatools/core.hpp"
#include "cgatools/reference/CrrFile.hpp"
#include "cgatools/cgdata/EvidenceReader.hpp"
#include "cgatools/util/BaseUtil.hpp"

Go to the source code of this file.

Classes
class	cgatools::mapping::AlleleSequenceAligner
	The class is used to iterate through the bases of a variation allele from an evidenceInterval file operator[] returns either a base from the allele or a reference base if the index points outside of the allele range. More...
class	cgatools::mapping::DnbSequenceIterator
	An iterator through an aligned read sequence The iterator is able to return bases in reverse order or/and complimented. More...
class	cgatools::mapping::GapAndConcordanceExtractor
	The class scans a given alignment for a given allele, provided by AlleleSequenceAligner in the constructor. More...
class	cgatools::mapping::GapProbabilityAndConcordanceExtractor
	The class extends GapAndConcordanceExtractor by computing the probablility of sequence-dependent gaps in addition to the metrics computed by the parent class. More...
Namespaces
namespace	cgatools
	Namespace containing the libcgatools API.
Defines
#define	CGA_TOOLS_ALLELE_ALIGNMENT_HPP_   1

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Detailed Description