def _read_call_freqs(in_file, sample_name): """Identify frequencies for calls in the input file. """ 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
def _read_call_freqs(in_file, sample_name): """Identify frequencies for calls in the input file. """ 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 = bubbletree.sample_alt_and_depth(sample) if depth > 0: out[_get_key(rec)] = float(alt) / float(depth) return out
def _read_call_freqs(in_file, sample_name): """Identify frequencies for calls in the input file. """ 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