code: def _nucmer_command(self, ref, qry, outprefix):
          '''Construct the nucmer command'''
          if self.use_promer:
              command = 'promer'
          else:
              command = 'nucmer'
  
          command += ' -p ' + outprefix
  
          if self.breaklen is not None:
              command += ' -b ' + str(self.breaklen)
  
          if self.diagdiff is not None and not self.use_promer:
              command += ' -D ' + str(self.diagdiff)
  
          if self.diagfactor:
              command += ' -d ' + str(self.diagfactor)
  
          if self.maxgap:
              command += ' -g ' + str(self.maxgap)
  
          if self.maxmatch:
              command += ' --maxmatch'
  
          if self.mincluster is not None:
              command += ' -c ' + str(self.mincluster)
  
          if not self.simplify and not self.use_promer:
          	command += ' --nosimplify'
  
          return command + ' ' + ref + ' ' + qrf _nucmer_command(self, ref, qry, outprefix):
          '''Construct the nucmer command'''
          if self.use_promer:
              command = 'promer'
          else:
              command = 'nucmer'
  
          command += ' -p ' + outprefix
  
          if self.breaklen is not None:
              command += ' -b ' + str(self.breaklen)
  
          if self.diagdiff is not None and not self.use_promer:
              command += ' -D ' + str(self.diagdiff)
  
          if self.diagfactor:
              command += ' -d ' + str(self.diagfactor)
  
          if self.maxgap:
              command += ' -g ' + str(self.maxgap)
  
          if self.maxmatch:
              command += ' --maxmatch'
  
          if self.mincluster is not None:
              command += ' -c ' + str(self.mincluster)
  
          if not self.simplify and not self.use_promer:
          	command += ' --nosimplify'
  
          return command + ' ' + ref + ' ' + qry
docs: Construct the nucmer command