def simplify_alleles(variant):
"""Replaces the alleles in variants with their simplified versions.
This function takes a variant and replaces its ref and alt alleles with those
produced by a call to variantutils.simplify_alleles() to remove common postfix
bases in the alleles that may be present due to pruning away alleles.
Args:
variant: learning.genomics.genomics.Variant proto we want to simplify.
Returns:
variant with its ref and alt alleles replaced with their simplified
equivalents.
"""
simplified_alleles = variantutils.simplify_alleles(
variant.reference_bases, *variant.alternate_bases)
variant.reference_bases = simplified_alleles[0]
variant.alternate_bases[:] = simplified_alleles[1:]
return variant
def test_simplify_alleles(self, alleles, expected):
self.assertEqual(variantutils.simplify_alleles(*alleles),
tuple(expected))
self.assertEqual(variantutils.simplify_alleles(*reversed(alleles)),
tuple(reversed(expected)))
def _simplify_alleles(variant, alleles):
return [
variantutils.simplify_alleles(variant.reference_bases, allele)
for allele in alleles
if allele != variant.reference_bases
]