def test_pedigree_with_gls():
ped = Pedigree(NumericSampleIds())
genotypes1 = [0, 1, 0, 2]
gls1 = [
PhredGenotypeLikelihoods(0, 1, 2),
PhredGenotypeLikelihoods(215, 81, 147),
PhredGenotypeLikelihoods(199, 49, 253),
PhredGenotypeLikelihoods(167, 200, 163),
]
genotypes5 = [1, 2, 2, 0]
gls5 = [
PhredGenotypeLikelihoods(184, 71, 233),
PhredGenotypeLikelihoods(65, 32, 87),
PhredGenotypeLikelihoods(28, 215, 131),
PhredGenotypeLikelihoods(98, 250, 137),
]
ped.add_individual('sample1', genotypes1, gls1)
assert len(ped) == 1
assert ped.variant_count == 4, str(ped.variant_count)
ped.add_individual('sample5', genotypes5, gls5)
assert len(ped) == 2
assert ped.variant_count == 4, str(ped.variant_count)
for i in range(ped.variant_count):
assert ped.genotype('sample1', i) == genotypes1[i]
assert list(ped.genotype_likelihoods('sample1', i)) == list(gls1[i])
assert ped.genotype('sample5', i) == genotypes5[i]
assert list(ped.genotype_likelihoods('sample5', i)) == list(gls5[i])
def test_pedigree_no_gls():
ped = Pedigree(NumericSampleIds())
genotypes1 = [0, 1, 0, 2]
genotypes5 = [1, 2, 2, 0]
ped.add_individual('sample1', genotypes1)
assert len(ped) == 1
assert ped.variant_count == 4, str(ped.variant_count)
ped.add_individual('sample5', genotypes5)
assert len(ped) == 2
assert ped.variant_count == 4, str(ped.variant_count)
for i in range(ped.variant_count):
assert ped.genotype('sample1', i) == genotypes1[i]
assert ped.genotype_likelihoods('sample1', i) is None
assert ped.genotype('sample5', i) == genotypes5[i]
assert ped.genotype_likelihoods('sample5', i) is None
