code: def reads_overlapping_variants(variants, samfile, **kwargs):
      
      chromosome_names = set(samfile.references)
      for variant in variants:
          # I imagine the conversation went like this:
          # A: "Hey, I have an awesome idea"
          # B: "What's up?"
          # A: "Let's make two nearly identical reference genomes"
          # B: "But...that sounds like it might confuse people."
          # A: "Nah, it's cool, we'll give the chromosomes different prefixes!"
          # B: "OK, sounds like a good idea."
          if variant.contig in chromosome_names:
              chromosome = variant.contig
          elif "chr" + variant.contig in chromosome_names:
              chromosome = "chr" + variant.contig
          else:
              logger.warn(
                  "Chromosome '%s' from variant %s not in alignment file %s",
                  chromosome,
                  variant,
                  samfile.filename)
              yield variant, []
              continue
          allele_reads = reads_overlapping_variant(
              samfile=samfile,
              chromosome=chromosome,
              variant=variant,
              **kwargs)
          yield variant, allele_reads
docs: Generates sequence of tuples, each containing a variant paired with
      a list of AlleleRead objects.
  
      Parameters
      ----------
      variants : varcode.VariantCollection
  
      samfile : pysam.AlignmentFile
  
      use_duplicate_reads : bool
          Should we use reads that have been marked as PCR duplicates
  
      use_secondary_alignments : bool
          Should we use reads at locations other than their best alignment
  
      min_mapping_quality : int
          Drop reads below this mapping quality