- fastqRead readFastq(ifstream&);
- vector< vector<string> > readFastqFiles(int&);
- bool checkReads(fastqRead&, fastqRead&);
- int createProcesses(vector< vector<string> >, string, string, string);
- int driver(vector<string>, string, string, string);
+ map<int, oligosPair> barcodes;
+ map<int, oligosPair> primers;
+ vector<string> linker;
+ vector<string> spacer;
+ vector<string> primerNameVector;
+ vector<string> barcodeNameVector;
+ vector<char> convertTable;
+
+ map<string, int> groupCounts;
+ map<string, string> groupMap;
+
+ vector<int> convertQual(string);
+ fastqRead readFastq(ifstream&, bool&);
+ 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);
+ string reverseOligo(string);
+ vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques);