docs: def vcf_line(input_data, reference):
      """
      Convert the var files information into VCF format.
  
      This is nontrivial because the var file can contain zero-length variants,
      which is not allowed by VCF. To handle these cases, we "move backwards"
      by one position, look up the reference sequence, and add that.
  
      The returned line is a very simple, VCF-valid row containing the
      genome's data for this position.
      """
      vcf_data = VCF_DATA_TEMPLATE.copy()
      start = int(input_data['start'])
      dbsnp_data = input_data['dbsnp_data']
      ref_allele = input_data['ref_seq']
      genome_alleles = input_data['alleles']
  
      # Get dbSNP IDs.
      dbsnp_cleaned = []
      for dbsnp in dbsnp_data:
          if dbsnp not in dbsnp_cleaned:
              dbsnp_cleaned.append(dbsnp)
      if dbsnp_cleaned:
          id_field = ';'.join(dbsnp_cleaned)
          if id_field == '':
              id_field = '.'
      else:
          id_field = '.'
  
      # Is this a matching reference line? Handle per gVCF spec.
      if input_data['ref_seq'] == '=':
          ref_allele = reference[input_data['chrom']][start].upper()
          vcf_data['CHROM'] = input_data['chrom']
  
          # Position notes: Complete Genomics uses 0-based start and 1-based end.
          # Reference seq retrieval is 0-based start, but VCF is 1-based start.
          vcf_data['POS'] = str(start + 1)
          vcf_data['ID'] = id_field
          vcf_data['REF'] = ref_allele
          vcf_data['ALT'] = '.'
          vcf_data['FORMAT'] = 'GT'
          assert input_data['allele_count'] in ['1', '2']
          if '?' in input_data['alleles']:
              if 'NOCALL' not in input_data['filters']:
                  input_data['filters'].append('NOCALL')
              if input_data['allele_count'] == '2':
                  vcf_data['SAMPLE'] = './.'
              else:
                  vcf_data['SAMPLE'] = '.'
          elif input_data['allele_count'] == '2':
              vcf_data['SAMPLE'] = '0/0'
          else:
              vcf_data['SAMPLE'] = '0'
  
          if input_data['filters']:
              vcf_data['FILTER'] = ';'.join(input_data['filters'])
          else:
              vcf_data['FILTER'] = 'PASS'
          vcf_data['INFO'] = 'END={}'.format(input_data['end'])
  
          return formatted_vcf_line(vcf_data)
  
      # VCF doesn't allow zero-length sequences. If we have this situation,
      # move the start backwards by one position, get that reference base,
      # and prepend this base to all sequences.
      if len(ref_allele) == 0 or 0 in [len(v) for v in genome_alleles]:
          start = start - 1
          prepend = reference[input_data['chrom']][start].upper()
          ref_allele = prepend + ref_allele
          genome_alleles = [prepend + v if v != '?' else v for v in
                            genome_alleles]
  
      # Figure out what our alternate alleles are.
      alt_alleles = []
      for allele in genome_alleles:
          if allele not in [ref_allele] + alt_alleles and allele != '?':
              alt_alleles.append(allele)
  
      # Combine ref and alt for the full set of alleles, used for indexing.
      alleles = [ref_allele] + alt_alleles
  
      # Get the indexed genotype.
      allele_indexes = [str(alleles.index(x)) for x in genome_alleles if
                        x != '?']
      [allele_indexes.append('.') for x in genome_alleles if x == '?']
      genotype = '/'.join(allele_indexes)
  
      vcf_data['CHROM'] = input_data['chrom']
      vcf_data['POS'] = str(start + 1)
      vcf_data['ID'] = id_field
      vcf_data['REF'] = ref_allele
      vcf_data['ALT'] = ','.join(alt_alleles) if alt_alleles else '.'
      vcf_data['FORMAT'] = 'GT'
      vcf_data['SAMPLE'] = genotype
  
      if input_data['filters']:
          vcf_data['FILTER'] = ';'.join(sorted(input_data['filters']))
      else:
          vcf_data['FILTER'] = 'PASS'
  
      return formatted_vcf_line(vcf_data)