- vector< vector<string> > readFastqFiles(unsigned long int&);
- bool checkReads(fastqRead&, fastqRead&);
- int createProcesses(vector< vector<string> >, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
- int driver(vector<string>, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
- bool getOligos(vector<vector<string> >&, vector<vector<string> >&);
+ vector< vector< vector<string> > > preProcessData(unsigned long int&);
+ vector< vector<string> > readFileNames(string);
+ vector< vector<string> > readFastqFiles(unsigned long int&, string, string);
+ vector< vector<string> > readFastaFiles(unsigned long int&, string, string);
+ //bool checkReads(fastqRead&, fastqRead&, string, string);
+ int createProcesses(vector< vector<string> >, string, string, string, vector<vector<string> >);
+ int driver(vector<string>, string, string, string, vector<vector<string> >, int);
+ bool getOligos(vector<vector<string> >&, string);