code: def _setup_variant_regions(data, out_dir):
      
      vr_file = dd.get_variant_regions(data)
      if not vr_file:
          vr_file = regions.get_sv_bed(data, "transcripts", out_dir=out_dir)
      contigs = set([c.name for c in ref.file_contigs(dd.get_ref_file(data))])
      out_file = os.path.join(utils.safe_makedir(os.path.join(dd.get_work_dir(data), "bedprep")),
                              "%s-rnaseq_clean.bed" % utils.splitext_plus(os.path.basename(vr_file))[0])
      if not utils.file_uptodate(out_file, vr_file):
          with file_transaction(data, out_file) as tx_out_file:
              with open(tx_out_file, "w") as out_handle:
                  with shared.bedtools_tmpdir(data):
                      for r in pybedtools.BedTool(vr_file):
                          if r.chrom in contigs:
                              if chromhacks.is_nonalt(r.chrom):
                                  out_handle.write(str(r))
      data = dd.set_variant_regions(data, out_file)
      return data
docs: Ensure we have variant regions for calling, using transcript if not present.
  
      Respects noalt_calling by removing additional contigs to improve
      speeds.