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;
vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;