code: def construct_nucmer_cmdline(
      fname1,
      fname2,
      outdir=".",
      nucmer_exe=pyani_config.NUCMER_DEFAULT,
      filter_exe=pyani_config.FILTER_DEFAULT,
      maxmatch=False,
  ):
      
      outsubdir = os.path.join(outdir, pyani_config.ALIGNDIR["ANIm"])
      outprefix = os.path.join(
          outsubdir,
          "%s_vs_%s"
          % (
              os.path.splitext(os.path.split(fname1)[-1])[0],
              os.path.splitext(os.path.split(fname2)[-1])[0],
          ),
      )
      if maxmatch:
          mode = "--maxmatch"
      else:
          mode = "--mum"
      nucmercmd = "{0} {1} -p {2} {3} {4}".format(
          nucmer_exe, mode, outprefix, fname1, fname2
      )
      filtercmd = "delta_filter_wrapper.py " + "{0} -1 {1} {2}".format(
          filter_exe, outprefix + ".delta", outprefix + ".filter"
      )
      return (nucmercmd, filtercmd)
docs: Returns a tuple of NUCmer and delta-filter commands
  
      The split into a tuple was made necessary by changes to SGE/OGE. The
      delta-filter command must now be run as a dependency of the NUCmer
      command, and be wrapped in a Python script to capture STDOUT.
  
      NOTE: This command-line writes output data to a subdirectory of the passed
      outdir, called "nucmer_output".
  
      - fname1 - query FASTA filepath
      - fname2 - subject FASTA filepath
      - outdir - path to output directory
      - maxmatch - Boolean flag indicating whether to use NUCmer's -maxmatch
      option. If not, the -mum option is used instead