Fix Python input conversion for methylation-aware phasing

deepvariant/python/BUILD

@@ -215,6 +215,17 @@ pybind_library(
     ],
 )
 
+py_test(
+    name = "methylation_aware_phasing_wrap_test",
+    srcs = ["methylation_aware_phasing_wrap_test.py"],
+    deps = [
+        ":methylation_aware_phasing",
+        "//deepvariant/protos:deepvariant_py_pb2",
+        "//third_party/nucleus/protos:reads_py_pb2",
+        "@absl_py//absl/testing:absltest",
+    ],
+)
+
 pybind_extension(
     name = "pileup_image_native",
     srcs = ["pileup_image_native_pybind.cc"],

deepvariant/python/methylation_aware_phasing_pybind.cc

@@ -36,6 +36,8 @@
 
 #include <pybind11/stl.h>
 
+#include <vector>
+
 #include "deepvariant/methylation_aware_phasing.h"
 #include "third_party/nucleus/core/python/type_caster_nucleus_status.h"
 #include "third_party/nucleus/core/python/type_caster_nucleus_statusor.h"
@@ -49,7 +51,13 @@ PYBIND11_MODULE(methylation_aware_phasing, m) {
   using namespace ::learning::genomics::deepvariant;  // NOLINT
 
   m.def("phase",
-        &PerformMethylationAwarePhasing,
+        [](const std::vector<nucleus::genomics::v1::Read>& reads_to_phase,
+           const std::vector<int>& initial_read_phases,
+           std::vector<DeepVariantCall>& methylated_ref_sites, int max_iter) {
+          return PerformMethylationAwarePhasing(
+              reads_to_phase, initial_read_phases, methylated_ref_sites,
+              max_iter);
+        },
         py::arg("reads_to_phase"),
         py::arg("initial_read_phases"),
         py::arg("methylated_ref_sites"),

deepvariant/python/methylation_aware_phasing_wrap_test.py

@@ -0,0 +1,76 @@
+# Copyright 2026 Google LLC.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+"""Tests for the methylation-aware phasing Python binding."""
+
+from absl.testing import absltest
+import numpy as np
+
+from deepvariant.protos import deepvariant_pb2
+from deepvariant.python import methylation_aware_phasing
+from third_party.nucleus.protos import reads_pb2
+
+
+class MethylationAwarePhasingWrapTest(absltest.TestCase):
+
+  def test_empty_inputs(self):
+    phases, p_values = methylation_aware_phasing.phase([], [], [])
+    self.assertEmpty(phases)
+    self.assertEmpty(p_values)
+
+  def test_reads_without_methylated_sites_preserve_initial_phases(self):
+    reads = [
+        reads_pb2.Read(fragment_name=f'read_{i}', read_number=1)
+        for i in range(3)
+    ]
+    phases, p_values = methylation_aware_phasing.phase(
+        reads, [1, 0, 2], []
+    )
+    self.assertEqual(phases, [1, 0, 2])
+    self.assertEmpty(p_values)
+
+  def test_accepts_numpy_candidate_array(self):
+    # RegionProcessor passes a NumPy array after selecting reference sites.
+    site = deepvariant_pb2.DeepVariantCall(methylation_p_value=0.25)
+    reads = [reads_pb2.Read(fragment_name='read', read_number=1)]
+    phases, p_values = methylation_aware_phasing.phase(
+        reads, [1], np.asarray([site], dtype=object)
+    )
+    self.assertEqual(phases, [1])
+    self.assertEqual(p_values, [0.25])
+
+  def test_accepts_empty_numpy_candidate_array(self):
+    phases, p_values = methylation_aware_phasing.phase(
+        [], [], np.asarray([], dtype=object)
+    )
+    self.assertEmpty(phases)
+    self.assertEmpty(p_values)
+
+
+if __name__ == '__main__':
+  absltest.main()