- string fastafile, namefile, groupfile;
- int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
+ string fastafile, namefile, groupfile, alignreport, outputDir;
+ int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
+ vector<string> outputNames;
+ vector<string> optimize;
+ map<string, vector<string> > outputTypes;
+
+ int getSummary(vector<unsigned long int>&);
+ int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);