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']
o.harmonicMean = args['displayHarmonicMean']
