def METHOD_NAME(inputFilename, arpFilename, windowSize, mapOrder, debug):
    haploParse = HaploArlequin(idCol = 1,
                               arpFilename = arpFilename,
                               prefixCols = 2,
                               suffixCols = 0,
                               windowSize = windowSize,
                               mapOrder = mapOrder,
                               debug=debug)
    haploParse.outputArlequin(open(inputFilename, 'r').readlines())
    haploParse.runArlequin()
    haplotypes = haploParse.METHOD_NAME()
    return haplotypes