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#include "NeighborSet.hpp"
#include "DNASeq.hpp"
using namespace std;
const unsigned int NeighborSet::MaxNNeighbors = 1000;
const unsigned int NeighborSetLoader::MaxSeqLen = 500;
const unsigned int NeighborSetLoader::CacheSize = 50000;
bool NeighborInfo::isNeighbor(const DNASeq& read1, const DNASeq& read2, int k, int h, float e) {
int st1 = get_st1();
int st2 = get_st2();
int overlap = get_overlap(read1.size(), read2.size());
if(overlap<h)
return false;
nerr = 0;
const char* seq1 = read1.getSeq();
const char* seq2 = read2.getSeq();
for(int i=0; i<overlap; i++)
if(seq1[st1+i]!=seq2[st2+i])
nerr++;
if(nerr>overlap*e)
return false;
return true;
}
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