def _create_cvo_proto(encoded_variant,
gls,
encoded_alt_allele_indices,
true_labels=None,
logits=None,
prelogits=None):
"""Returns a CallVariantsOutput proto from the relevant input information."""
variant = variants_pb2.Variant.FromString(encoded_variant)
alt_allele_indices = (deepvariant_pb2.CallVariantsOutput.AltAlleleIndices.
FromString(encoded_alt_allele_indices))
debug_info = None
if FLAGS.include_debug_info or FLAGS.debugging_true_label_mode:
if prelogits is not None:
assert prelogits.shape == (1, 1, 2048)
prelogits = prelogits[0][0]
debug_info = deepvariant_pb2.CallVariantsOutput.DebugInfo(
has_insertion=variant_utils.has_insertion(variant),
has_deletion=variant_utils.has_deletion(variant),
is_snp=variant_utils.is_snp(variant),
predicted_label=np.argmax(gls),
true_label=true_labels,
logits=logits,
prelogits=prelogits)
call_variants_output = deepvariant_pb2.CallVariantsOutput(
variant=variant,
alt_allele_indices=alt_allele_indices,
genotype_probabilities=gls,
debug_info=debug_info)
return call_variants_output
def test_exception_extract_single_variant_name(self, names):
variant_calls = [
variants_pb2.VariantCall(call_set_name=name) for name in names
]
variant = variants_pb2.Variant(calls=variant_calls)
record = deepvariant_pb2.CallVariantsOutput(variant=variant)
with self.assertRaisesRegexp(ValueError, 'Expected exactly one VariantCal'):
postprocess_variants._extract_single_sample_name(record)
def _create_call_variants_output(indices,
probabilities,
ref=None,
alts=None,
variant=None):
if alts is None != variant is None:
raise ValueError('Exactly one of either `alts` or `variant` should be set.')
if not variant:
variant = _create_variant_with_alleles(ref=ref, alts=alts)
return deepvariant_pb2.CallVariantsOutput(
genotype_probabilities=probabilities,
alt_allele_indices=deepvariant_pb2.CallVariantsOutput.AltAlleleIndices(
indices=indices),
variant=variant)
def _create_cvo_proto(encoded_variant, gls, encoded_alt_allele_indices):
"""Returns a CallVariantsOutput proto from the relevant input information."""
variant = variants_pb2.Variant.FromString(encoded_variant)
alt_allele_indices = (deepvariant_pb2.CallVariantsOutput.AltAlleleIndices.
FromString(encoded_alt_allele_indices))
debug_info = None
if FLAGS.include_debug_info:
debug_info = deepvariant_pb2.CallVariantsOutput.DebugInfo(
has_insertion=variantutils.has_insertion(variant),
has_deletion=variantutils.has_deletion(variant),
is_snp=variantutils.is_snp(variant),
predicted_label=np.argmax(gls))
call_variants_output = deepvariant_pb2.CallVariantsOutput(
variant=variant,
alt_allele_indices=alt_allele_indices,
genotype_probabilities=gls,
debug_info=debug_info)
return call_variants_output
def write_output(encoded_variant, gls, encoded_alt_allele_indices):
"""Provides a write function for a CallVariantsOutput proto."""
variant = variants_pb2.Variant.FromString(encoded_variant)
alt_allele_indices = (
deepvariant_pb2.CallVariantsOutput.AltAlleleIndices.FromString(
encoded_alt_allele_indices))
debug_info = None
if FLAGS.include_debug_info:
debug_info = deepvariant_pb2.CallVariantsOutput.DebugInfo(
has_insertion=variantutils.has_insertion(variant),
has_deletion=variantutils.has_deletion(variant),
is_snp=variantutils.is_snp(variant),
predicted_label=np.argmax(gls))
call_variants_output = deepvariant_pb2.CallVariantsOutput(
variant=variant,
alt_allele_indices=alt_allele_indices,
genotype_probabilities=gls,
debug_info=debug_info)
write_fn(call_variants_output)
