+ string outputDir, fastaQFile, format, oligosfile, groupfile;
+ bool abort, fasta, qual, pacbio, pairedOligos;
+ int pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, split;
+ GroupMap* groupMap;
+
+ //oligos file data structures
+ vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
+ map<string, int> barcodes;
+ map<string, int> primers;
+ map<int, oligosPair> pairedBarcodes;
+ map<int, oligosPair> pairedPrimers;
+ vector<vector<string> > fastqFileNames;
+ string noMatchFile;