code: def _prep_genome(out_dir, data):
      
      genome_name = utils.splitext_plus(os.path.basename(dd.get_ref_file(data)))[0]
      out_dir = utils.safe_makedir(os.path.join(out_dir, genome_name))
      ref_file = dd.get_ref_file(data)
      utils.symlink_plus(ref_file, os.path.join(out_dir, os.path.basename(ref_file)))
      with open(os.path.join(out_dir, "GenomeSize.xml"), "w") as out_handle:
          out_handle.write('<sequenceSizes genomeName="%s">' % genome_name)
          for c in pysam.AlignmentFile("%s.dict" % utils.splitext_plus(ref_file)[0]).header["SQ"]:
              cur_ploidy = ploidy.get_ploidy([data], region=[c["SN"]])
              out_handle.write('<chromosome fileName="%s" contigName="%s" totalBases="%s" knownBases="%s" '
                               'isCircular="false" ploidy="%s" md5="%s"/>' %
                               (os.path.basename(ref_file), c["SN"], c["LN"], c["LN"], cur_ploidy, c["M5"]))
          out_handle.write('</sequenceSizes>')
      return out_dir
docs: Create prepped reference directory for pisces.
  
      Requires a custom GenomeSize.xml file present.