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 test_haploid_allele_indices_for_genotype_likelihood_index(self):
for aix in 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 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 add(self, allele_indices, likelihood):
"""Add some likelihood to a particular allele configuration.
Args:
allele_indices: Pair of (g1, g2) ints representing the genotype.
likelihood: float. log10(probability of this genotype configuration).
"""
ix = variant_utils.genotype_likelihood_index(allele_indices)
self._genotype_likelihood_containers[ix].append(likelihood)
def test_diploid_allele_indices_for_genotype_likelihood_index(self):
for aix in xrange(20):
for bix in xrange(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 __init__(self, num_alts):
"""Constructor.
Args:
num_alts: int. The number of alternate alleles in the variant.
"""
self._num_likelihoods = variant_utils.genotype_likelihood_index(
(num_alts, num_alts)) + 1
# At each GL index, we keep a list that will include the joint GL across all
# variants that include that particular set of allele indices for this
# variant.
self._genotype_likelihood_containers = []
for _ in xrange(self._num_likelihoods):
self._genotype_likelihood_containers.append([])
