class TestVariantTyperWithMultipleProbeCoverages(TestCase):
def setUp(self):
self.vt_no_contaim = VariantTyper(expected_depths=[100],
contamination_depths=[])
def teardown(self):
pass
def test_simple_case(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=80,
median_depth=80,
k_count=80,
klen=31)
alt1 = ProbeCoverage(min_depth=100,
percent_coverage=50,
median_depth=20,
k_count=20,
klen=31)
alt2 = ProbeCoverage(min_depth=100,
percent_coverage=40,
median_depth=80,
k_count=30,
klen=31)
alternate_coverages = [alt1, alt2]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=80,
median_depth=80,
k_count=20,
klen=31)
alt1 = ProbeCoverage(min_depth=100,
percent_coverage=50,
median_depth=20,
k_count=20,
klen=31)
alt2 = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=80,
k_count=100,
klen=31)
alternate_coverages = [alt1, alt2]
v2 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type([v1, v2])
assert call['genotype'] == [1, 1]
def setUp(self):
self.vt = VariantTyper(expected_depths=[100])