def test_haploid_allele_indices_for_genotype_likelihood_index(self):
for aix in six.moves.xrange(20):
allele_indices = (aix,)
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=1)
self.assertEqual(actual, aix)
def recall_variant(log_priors, variant):
"""Update the genotype calls in variant given the new genotype priors."""
for call in variant.calls:
if len(log_priors) != len(call.genotype_likelihood):
continue
posteriors = [
x + y for x, y in zip(log_priors, call.genotype_likelihood)
]
sorted_posts = sorted(posteriors)
highest_post = sorted_posts[-1]
margin = 0
if FLAGS.posterior_margin > 0.0 and len(log_priors) > 1:
margin = math.pow(10.0, highest_post) - math.pow(
10.0, sorted_posts[-2])
ploidy = variantcall_utils.ploidy(call)
if margin < FLAGS.posterior_margin:
call.genotype[:] = [-1] * ploidy
else:
best_genotype = posteriors.index(highest_post)
call.genotype[:] = (
variant_utils.allele_indices_for_genotype_likelihood_index(
best_genotype, ploidy=ploidy))
def test_diploid_allele_indices_for_genotype_likelihood_index(self):
for aix in range(20):
for bix in range(20):
allele_indices = (aix, bix)
expected = tuple(sorted(allele_indices))
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=2)
self.assertEqual(actual, expected)
def test_unsupported_allele_indices_for_genotype_likelihood_index(
self, ploidy):
with self.assertRaisesRegexp(NotImplementedError,
'only supported for haploid and diploid'):
variant_utils.allele_indices_for_genotype_likelihood_index(0, ploidy)
