- string outputDir, fastaQFile;
- bool abort, fasta, qual;
+ string outputDir, fastaQFile, format, oligosfile, groupfile;
+ bool abort, fasta, qual, pacbio, pairedOligos, reorient;
+ int pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, split, numBarcodes, numPrimers, numLinkers, numSpacers, numRPrimers;
+ GroupMap* groupMap;
+ Oligos oligos;
+
+ vector<vector<string> > fastqFileNames;
+ string noMatchFile;