code: def _prep_cnv_file(in_file, work_dir, somatic_info):
      
      out_file = os.path.join(work_dir, "%s-prep%s" % utils.splitext_plus(os.path.basename(in_file)))
      if not utils.file_uptodate(out_file, in_file):
          with file_transaction(somatic_info.tumor_data, out_file) as tx_out_file:
              with open(in_file) as in_handle:
                  with open(tx_out_file, "w") as out_handle:
                      out_handle.write(in_handle.readline())  # header
                      for line in in_handle:
                          parts = line.split("\t")
                          parts[1] = _phylowgs_compatible_chroms(parts[1])
                          out_handle.write("\t".join(parts))
      return out_file
docs: Prepare Battenberg CNV file for ingest by PhyloWGS.
  
      The PhyloWGS preparation script does not handle 'chr' prefixed chromosomes (hg19 style)
      correctly. This converts them over to GRCh37 (no 'chr') style to match preparation
      work in _prep_vrn_file.