code: def get_ref_haplotype_and_offset(
      dv_variant, cohort_variants, ref_reader
  ):
      """Gets reference haplotype that overlaps with given variants and its offset.
  
      Reference offset is the starting position of the returned haplotype.
      It is the minimal starting positions of dv_variant and cohort_variants.
      Reference haplotype is the reference sequence from reference_offset to the
      maximal ending position of dv_variant and cohort_variants.
  
      Args:
        dv_variant: A Variant proto.
        cohort_variants: A list of Variant protos.
        ref_reader: A fasta.IndexedFastaReader.
  
      Returns:
        A tuple of a string and an integer.
          - String: Reference haplotype overlapping with dv_variant and
                    cohort_variants.
          - Integer: Offset of the reference haplotype.
  
      Raises:
        ValueError: If the queried region is invalid.
      """
      # Get the range for haplotypes to be compared.
      min_start_position = min(
          dv_variant.start, min([cv.start for cv in cohort_variants])
      )
      max_end_position = max(
          dv_variant.end, max([cv.end for cv in cohort_variants])
      )
  
      haplotype_region = ranges.make_range(
          dv_variant.reference_name,
          min_start_position,
          max_end_position,
      )
  
      if ref_reader.is_valid(haplotype_region):
          return ref_reader.query(haplotype_region), min_start_position
      else:
          raise ValueError(
              "Invalid IndexedFastaReader region", haplotype_region
          )
  
file_path: deepvariant/deepvariant/allele_frequency.py
imports: import collections
  from typing import DefaultDict, Sequence, Optional
  from absl import logging
  from third_party.nucleus.io import vcf
  from third_party.nucleus.util import ranges
  from third_party.nucleus.util import variant_utils
  from deepvariant.protos import deepvariant_pb2
label_desc: Use image node_id 3 for calling a global function with example usage: get_ref_haplotype_and_offset(dv_variant, cohort_variants, ref_reader) and returns: ref_reader,  min_start_position