+ void removeBadReferenceSeqs(vector<Sequence*>&, int); //removes sequences from closest that are to different of too similar to eachother.
+ void trimSequences();
+ vector<int> findWindows();
+ vector<float> getAverageRef(vector<Sequence*>);
+ vector<float> getAverageQuery (vector<Sequence*>, int);
+
+
+ int getDiff(string, string); //return number of mismatched bases, a gap to base is not counted as a mismatch