code: def _read_call_freqs(in_file, sample_name):
      
      from bcbio.heterogeneity import bubbletree
      out = {}
      with VariantFile(in_file) as call_in:
          for rec in call_in:
              if rec.filter.keys() == ["PASS"]:
                  for name, sample in rec.samples.items():
                      if name == sample_name:
                          alt, depth, freq = bubbletree.sample_alt_and_depth(rec, sample)
                          if freq is not None:
                              out[_get_key(rec)] = freq
      return out
docs: Identify frequencies for calls in the input file.