code: def get_noalt_contigs(data):
      
      alts = set([])
      alt_files = [f for f in tz.get_in(["reference", "bwa", "indexes"], data, []) if f.endswith("alt")]
      if alt_files:
          for alt_file in alt_files:
              with open(alt_file) as in_handle:
                  for line in in_handle:
                      if not line.startswith("@"):
                          alts.add(line.split()[0].strip())
      else:
          for contig in ref.file_contigs(dd.get_ref_file(data)):
              if ("_alt" in contig.name or "_decoy" in contig.name or
                    contig.name.startswith("HLA-") or ":" in contig.name):
                  alts.add(contig.name)
      return [c for c in ref.file_contigs(dd.get_ref_file(data)) if c.name not in alts]
docs: Retrieve contigs without alternatives as defined in bwa *.alts files.
  
      If no alt files present (when we're not aligning with bwa), work around
      with standard set of alts based on hg38 -- anything with HLA, _alt or
      _decoy in the name.