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//
// compare.h
// Mothur
//
// Created by Sarah Westcott on 6/5/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#ifndef compare_h
#define compare_h
#include "mothurout.h"
//***************************************************************************************************************
struct Compare {
Compare(){
AA=0; AT=0; AG=0; AC=0;
TA=0; TT=0; TG=0; TC=0;
GA=0; GT=0; GG=0; GC=0;
CA=0; CT=0; CG=0; CC=0;
NA=0; NT=0; NG=0; NC=0;
Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
dA=0; dT=0; dG=0; dC=0;
refName = "";
queryName = "";
weight = 1;
matches = 0;
mismatches = 0;
total = 0;
errorRate = 1.0000;
sequence = "";
}
~Compare(){}
int AA, AT, AG, AC, TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
string refName, queryName, sequence;
double errorRate;
int weight, matches, mismatches, total;
};
//***************************************************************************************************************
#endif /* compare_h */
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