code: def _freqs_by_chromosome(in_file, params, somatic_info):
      
      freqs = []
      coords = []
      cur_chrom = None
      with pysam.VariantFile(in_file) as bcf_in:
          for rec in bcf_in:
              if _is_biallelic_snp(rec) and _passes_plus_germline(rec) and chromhacks.is_autosomal(rec.chrom):
                  if cur_chrom is None or rec.chrom != cur_chrom:
                      if cur_chrom and len(freqs) > 0:
                          yield cur_chrom, freqs, coords
                      cur_chrom = rec.chrom
                      freqs = []
                      coords = []
                  stats = _tumor_normal_stats(rec, somatic_info)
                  if tz.get_in(["tumor", "depth"], stats, 0) > params["min_depth"]:
                      # not a ref only call
                      if len(rec.samples) == 0 or sum(rec.samples[somatic_info.tumor_name].allele_indices) > 0:
                          freqs.append(tz.get_in(["tumor", "freq"], stats))
                          coords.append(rec.start)
          if cur_chrom and len(freqs) > 0:
              yield cur_chrom, freqs, coords
docs: Retrieve frequencies across each chromosome as inputs to HMM.