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);
int driver(vector<string>, string, string, string, vector<vector<string> >, int, string);
bool getOligos(vector<vector<string> >&, string);
string reverseOligo(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);
int driver(vector<string>, string, string, string, vector<vector<string> >, int, string);
bool getOligos(vector<vector<string> >&, string);
string reverseOligo(string);