code: def _clean_freebayes_output(line):
      
      if line.startswith("#"):
          line = line.replace("Type=Int,D", "Type=Integer,D")
          return line
      else:
          parts = line.split("\t")
          alleles = [x.strip() for x in parts[4].split(",")] + [parts[3].strip()]
          if len(alleles) == len(set(alleles)):
              return line
      return None
docs: Clean FreeBayes output to make post-processing with GATK happy.
  
      XXX Not applied on recent versions which fix issues to be more compatible
      with bgzip output, but retained in case of need.
  
      - Remove lines from FreeBayes outputs where REF/ALT are identical:
        2       22816178        .       G       G       0.0339196
        or there are multiple duplicate alleles:
        4       60594753        .       TGAAA   T,T
      - Remove Type=Int specifications which are not valid VCF and GATK chokes
        on.