- string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile;
- vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
- bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;
+ string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile, groupfile;
+ vector<string> filenames, outputNames, accnosFileNames, oligosFileNames, groupFileNames;
+ bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos, hasGroup;