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#ifndef KMER_HPP
#define KMER_HPP
/*
* kmer.hpp
*
*
* Created by Pat Schloss on 12/15/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "mothur.h"
/**************************************************************************************************/
class Kmer {
public:
Kmer(int);
~Kmer() = default;
string getKmerString(string);
int getKmerNumber(string, int);
string getKmerBases(int);
int getReverseKmerNumber(int);
vector< map<int, int> > getKmerCounts(string sequence); //for use in chimeraCheck
private:
char getASCII(int);
int getNumber(char);
int kmerSize;
int maxKmer;
int nKmers;
};
/**************************************************************************************************/
#endif
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