def makeConsensusSeq(self, outDir):
        """
        multiple sequence alignment based
        """


        ## A) Single sequence
        if len(self.clippedReadDict.keys()) == 1:    
            consensusSeq = list(self.clippedReadDict.values())[0]["seq"].upper()

        ## B) Multiple sequence
        else:
            command = 'mkdir -p ' + outDir 
            os.system(command) # returns the exit status