def test_split_genotype_likelihood_with_missing_genotype_likelihood_diploid(self, log):
split_func = make_split_sample_alt_func("G", lambda x: x)
self.assertEqual(
[[None, None, None], [None, None, None]],
split_func([1.0, 2.0, 3.0], 2, GenotypeCall("0/1"))
)
log.check(
('wecall.vcfutils.fieldmetadata', 'WARNING',
"Incorrect number of values 'G' cardinality, expected 6, got 3"),
)
def test_split_genotype_likelihood_warns_for_non_haploid_diploid(self, log):
split_func = make_split_sample_alt_func("G", lambda x: x)
self.assertEqual(
[[1.0, 2.0], [1.0, 2.0]],
split_func([1.0, 2.0], 2, GenotypeCall("0/1/2"))
)
log.check(
('wecall.vcfutils.fieldmetadata', 'WARNING',
"Unable to handle ploidy other than haploid or diploid."),
)
def test_split_genotype_likelihood_warns_for_no_genotype(self, log):
split_func = make_split_sample_alt_func("G", lambda x: x)
self.assertEqual(
[[1.0, 2.0], [1.0, 2.0]],
split_func([1.0, 2.0], 2, None)
)
log.check(
('wecall.vcfutils.fieldmetadata', 'WARNING',
"Unknown ploidy when parsing genotype likelihood"),
)
def test_split_genotype_likelihood_with_correct_number_of_genotypes_diploid(self):
split_func = make_split_sample_alt_func("G", lambda x: x)
self.assertEqual([[1.0, 2.0, 3.0]], split_func(
[1.0, 2.0, 3.0], 1, GenotypeCall("0/1")))