bool abort, isSFF, pairedOligos;
int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
string sfffile, fastqfile, outputDir, file, oligosfile, contactfile, inputfile, mimarksfile;
bool abort, isSFF, pairedOligos;
int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
string sfffile, fastqfile, outputDir, file, oligosfile, contactfile, inputfile, mimarksfile;