printError(msg) if args['fragments'] == "" and args['detailedFrag'] == "" and args['fragSize'] == (-1): fragSize = default_fragmentSize elif args['fragSize'] > 0: fragSize = args['fragSize'] else: fragSize = (-1) # Writing the options into the Options clasee o.exePath = path.abspath(args['exe']) o.keepTemp = args['keepTempFiles'] o.threads = int(args['threads']) o.nice = args['nice'] o.skipREMO = args['NoREMO'] o.outData = args['outData'] o.inData = args['inData'] o.convert = args['convertToNewDataformat'] o.inCount = args['inCount'] o.inInfo = args['inInfo'] o.detailFrag = args['detailedFrag'] o.REMOout = args['REMOout'] o.pdt = args['pdt'] # o.distAnaly = args['analyseDistribution'] # o.fragDisAn = args['analyseFragmentDistribution'] # o.distAnSt = args['distributionStep'] o.filtOutl = args['filterOutliers'] o.outpOutl = args['outputOutliers'] o.translation = args['translation'] o.onlyTrans = args['translationOnly'] o.outDataTable = args['dumpDataTable'] o.verbData = args['outputAdditionalData']