+ ReferenceDB* rdb;
+
+ struct linePair {
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+ ~linePair(){}
+ };
+
+ struct 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;
+
+ 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(){};
+ };
+
+ vector<int> processIDS; //processid
+ vector<linePair> lines;
+ vector<linePair> qLines;
+ vector<linePair> rLines;