- int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
- int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
+ int getAlignedMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
+ int analyzeAlignedQuery(string, string, ofstream&);
+ int analyzeUnalignedQuery(string, string, ofstream&);
+ double alignQueryToReferences(string, string, string&, string&, double&);
+ int getUnalignedDiffs(string, string, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
+
+ int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);