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#ifndef _BLASR_ANCHOR_PARAMETERS_HPP_
#define _BLASR_ANCHOR_PARAMETERS_HPP_
#include <fstream>
#include <iostream>
#include "../../pbdata/qvs/QualityValue.hpp"
#include "../../pbdata/DNASequence.hpp"
class AnchorParameters {
public:
QualityValue branchQualityThreshold;
DNALength minMatchLength;
int maxMatchScore;
int expand;
int contextAlignLength;
bool useLookupTable;
int numBranches;
int maxAnchorsPerPosition;
int advanceExactMatches;
DNALength maxLCPLength;
bool stopMappingOnceUnique;
int verbosity;
bool removeEncompassedMatches;
std::ostream *lcpBoundsOutPtr;
int branchExpand;
AnchorParameters();
AnchorParameters &Assign(const AnchorParameters &rhs);
AnchorParameters &operator=(const AnchorParameters &rhs);
};
#endif // _BLASR_ANCHOR_PARAMETERS_HPP_
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