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#ifndef KMERALIGN_N
#define KMERALIGN_N
/*
* kmeralign.h
*
*
* Created by Pat Schloss on 4/6/14.
* Copyright 2014 Patrick D. Schloss. All rights reserved.
*
* This class is an Alignment child class that implements a kmer-based pairwise alignment algorithm
* for making contigs of reads without insertions
*
*
*/
#include "alignment.hpp"
#include "kmer.hpp"
# define PHREDMAX 46
# define PHREDCLAMP(x) ((x) > PHREDMAX ? PHREDMAX : ((x) < 0 ? 0 : (x)))
/**************************************************************************************************/
class KmerAlign : public Alignment {
public:
KmerAlign(int);
~KmerAlign();
void align(string, string, bool createBaseMap=false);
private:
int kmerSize;
int maxKmer;
Kmer kmerLibrary;
double calcProb(string A, string B, int overlap);
};
/**************************************************************************************************/
#endif
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