+ vector<Sequence> findClosest(Sequence, vector<Sequence*>&, vector<Sequence*>&, int, int); //takes querySeq, a reference db, filteredRefDB, numWanted, minSim
+ Sequence* findClosest(Sequence*, vector<Sequence*>);
+ set<int> getPos() { return h; }
+ void setMask(string);
+ void setAlignmentLength(int l) { alignLength = l; }