def test_sample_data_copes_with_mixed_missing_values_in_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.set_genotype_likelihoods(sample_name,
[-0.1, '.', -0.2, None, -0.3])
self.assertEqual(sample_data.get_field(sample_name, 'PL'),
[1.0, None, 2.0, None, 3.0])
def test_gets_dot_if_key_is_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.set_genotype_likelihoods(sample_name, '.')
self.assertEqual(sample_data.get_field(sample_name, 'PL'), '.')
def test_gets_exact_values_if_key_is_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.set_genotype_likelihoods(sample_name, [-0.1, -0.2, -0.3])
self.assertEqual(sample_data.get_field(sample_name, 'PL'), [1, 2, 3])