- string sffFilename, sfftxtFilename, outputDir, accnosName;
- vector<string> filenames, outputNames, accnosFileNames;
- bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
- int mycount;
+ string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile;
+ vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
+ bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;
+ int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs;