float minDivR, percentIdenticalQueryChimera;
vector<results> outputResults;
map<int, int> spotMap;
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+ vector<int> unalignedMap;
vector<Sequence*> minCoverageFilter(vector<Sequence*>); //removes top matches that do not have minimum coverage with query.
int computeChimeraPenalty();
void verticalFilter(vector<Sequence*>);