Rename variant_utils.has_genotypes to has_calls to reflect its fu…

…nction.

PiperOrigin-RevId: 188493871

deepvariant/labeler/positional_labeler.py

@@ -200,7 +200,9 @@ def _genotype_from_matched_truth(candidate_variant, truth_variant):
     raise ValueError('candidate_variant cannot be None')
   if truth_variant is None:
     raise ValueError('truth_variant cannot be None')
-  if not variant_utils.has_genotypes(truth_variant):
+  # redacted
+  if not (truth_variant.calls and
+          any(gt >= 0 for gt in truth_variant.calls[0].genotype)):
     raise ValueError('truth_variant needs genotypes to be used for labeling',
                      truth_variant)
 

deepvariant/labeler/variant_labeler.py

@@ -187,7 +187,9 @@ def _genotype_from_matched_truth(candidate_variant, truth_variant):
     raise ValueError('candidate_variant cannot be None')
   if truth_variant is None:
     raise ValueError('truth_variant cannot be None')
-  if not variant_utils.has_genotypes(truth_variant):
+  # redacted
+  if not (truth_variant.calls and
+          any(gt >= 0 for gt in truth_variant.calls[0].genotype)):
     raise ValueError('truth_variant needs genotypes to be used for labeling',
                      truth_variant)
 

deepvariant/util/variant_utils.py

@@ -520,14 +520,14 @@ def is_variant_call(variant,
     return False
 
 
-def has_genotypes(variant):
-  """Does variant have genotype calls?
+def has_calls(variant):
+  """Does variant have any genotype calls?
 
   Args:
     variant: third_party.nucleus.protos.Variant.
 
   Returns:
-    True if variant has genotype calls.
+    True if variant has one or more VariantCalls.
   """
   # I don't want to return the actual data structure so I'm doing the
   # explicit True/False evaluation here.
@@ -551,7 +551,7 @@ def genotype_type(variant):
   Raises:
     ValueError: If variant has more than one call (i.e., is multi-sample).
   """
-  if not has_genotypes(variant):
+  if not has_calls(variant):
     return GenotypeType.no_call
   elif len(variant.calls) > 1:
     raise ValueError('Unsupported: multiple genotypes found at', variant)
@@ -586,7 +586,7 @@ def genotype_as_alleles(variant):
     ValueError: If variant doesn't have genotypes.
     ValueError: If variant has more than one call (i.e., is multi-sample).
   """
-  if not has_genotypes(variant):
+  if not has_calls(variant):
     raise ValueError('Not genotypes present in', variant)
   elif len(variant.calls) > 1:
     raise ValueError('Unsupported: multiple genotypes found at', variant)
@@ -615,7 +615,7 @@ def genotype_quality(variant, default=None):
   Returns:
     The GQ value (may be a string or whatever value default is).
   """
-  if not has_genotypes(variant):
+  if not has_calls(variant):
     return default
   call = variant.calls[0]
   if 'GQ' in call.info:

deepvariant/util/variant_utils_test.py

@@ -396,13 +396,20 @@ def test_has_insertion_deletion(self, variant, has_insertion, has_deletion):
       (test_utils.make_variant(gt=[0, 1]), True),
       (test_utils.make_variant(gt=[1, 1]), True),
       (test_utils.make_variant(gt=[-1, -1]), True),
+      (variants_pb2.Variant(calls=[]), False),
+      (variants_pb2.Variant(
+          calls=[variants_pb2.VariantCall(call_set_name='no_geno')]), True),
+      (variants_pb2.Variant(calls=[
+          variants_pb2.VariantCall(call_set_name='no_geno'),
+          variants_pb2.VariantCall(call_set_name='no_geno2'),
+      ]), True),
   )
-  def test_has_genotypes(self, variant, expected):
-    self.assertEqual(variant_utils.has_genotypes(variant), expected)
+  def test_has_calls(self, variant, expected):
+    self.assertEqual(variant_utils.has_calls(variant), expected)
 
-  def test_has_genotypes_raises_with_bad_inputs(self):
+  def test_has_calls_raises_with_bad_inputs(self):
     with self.assertRaises(Exception):
-      variant_utils.has_genotypes(None)
+      variant_utils.has_calls(None)
 
   @parameterized.parameters(
       (test_utils.make_variant(gt=None), variant_utils.GenotypeType.no_call),