code: def merge_radia(job, perchrom_rvs):
      job.fileStore.logToMaster('Running merge_radia')
      work_dir = job.fileStore.getLocalTempDir()
      input_files = {filename: jsid for perchrom_files in perchrom_rvs.values()
                     for filename, jsid in perchrom_files.items()}
      input_files = get_files_from_filestore(job, input_files, work_dir,
                                             docker=False)
      chromosomes = [''.join(['chr', str(x)]) for x in range(1, 23) + ['X', 'Y']]
      with open('/'.join([work_dir, 'radia_calls.vcf']), 'w') as radfile, \
              open('/'.join([work_dir, 'radia_filter_passing_calls.vcf']), 'w') as radpassfile:
          for chrom in chromosomes:
              with open(input_files[''.join(['radia_filtered_', chrom, '.vcf'])], 'r') as filtradfile:
                  for line in filtradfile:
                      line = line.strip()
                      if line.startswith('
                          if chrom == 'chr1':
                              print(line, file=radfile)
                              print(line, file=radpassfile)
                          continue
                      else:
                          print(line, file=radfile)
                          line = line.split('\t')
                          if line[6] == 'PASS' and 'MT=GERM' not in line[7]:
                              print('\t'.join(line), file=radpassfile)
      with open(radpassfile.name, 'r') as radpassfile, \
              open('/'.join([work_dir, 'radia_parsed_filter_passing_calls.vcf']),
                   'w') as parsedradfile:
          parse_radia_multi_alt(radpassfile, parsedradfile)
      output_files = defaultdict()
      for radia_file in [radfile.name, parsedradfile.name]:
          output_files[os.path.basename(radia_file)] = job.fileStore.writeGlobalFile(radia_file)
      return output_files