def is_variant_call(variant,
require_non_ref_genotype=True,
no_calls_are_variant=False,
call_indices=None):
"""Is variant a non-reference call?
A Variant proto doesn't always imply that there's a variant present in the
genome. The call may not have alternate bases, may be filtered, may a have
hom-ref genotype, etc. This function looks for all of those configurations
and returns true iff the variant is asserting that a mutation is present
in the same.
Note that this code allows a variant without a calls field to be variant,
but one with a genotype call must have a non-reference genotype to be
considered variant (if require_non_ref_genotype is True, the default). If
False, a variant that passes all of the site-level requirements for being
a variant_call will return a True value, regardless of the genotypes, which
means that we'll consider a site with a sample with a hom-ref or no-call site
a variant call.
Args:
variant: nucleus.genomics.v1.Variant.
require_non_ref_genotype: Should we require a site with a genotype call to
have a non-reference (het, hom-var) genotype for the site to be considered
a variant call?
no_calls_are_variant: If a site has genotypes, should we consider no_call
genotypes as being variant or not?
call_indices: A list of 0-based indices. If specified, only the calls
at the given indices will be considered. The function will return
True if any of those calls are variant.
Returns:
True if variant is really a mutation call.
"""
if not variant.alternate_bases:
return False
elif is_filtered(variant):
return False
elif not variant.calls or not require_non_ref_genotype:
return True
# All tests after this point should only look at genotype-based fields, as
# we may have aborted out in the prev. line due to require_non_ref_genotype.
else:
if call_indices is None:
call_indices = range(len(variant.calls))
return any(
any(g > 0
for g in variant.calls[i].genotype) or
(no_calls_are_variant and
not variantcall_utils.has_genotypes(variant.calls[i]))
for i in call_indices)
def test_has_genotypes(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.has_genotypes(call)
self.assertEqual(actual, expected)