private:
bool abort, allFiles, createGroup;
- string outputDir, ffastqfile, rfastqfile, align, oligosfile;
+ string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file;
float match, misMatch, gapOpen, gapExtend;
int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
vector<string> outputNames;
//vector<string> groupVector;
fastqRead readFastq(ifstream&, bool&);
- vector< vector<string> > readFastqFiles(int&);
+ 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> >);