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 * modification, are permitted provided that the following conditions
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 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
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 * 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
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 *    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
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 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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#include "pybind11/cast.h"
#if true  // Trick to stop tooling from moving the #include around.
// MUST appear before any standard headers are included.
#include <pybind11/pybind11.h>
#endif

#include <pybind11/stl.h>

#include "deepvariant/direct_phasing.h"
#include "third_party/nucleus/core/python/type_caster_nucleus_status.h"
#include "third_party/nucleus/core/python/type_caster_nucleus_statusor.h"
#include "third_party/nucleus/util/python/type_caster_nucleus_proto_ptr.h"
#include "pybind11_protobuf/native_proto_caster.h"

namespace py = pybind11;

PYBIND11_MODULE(direct_phasing, m) {
  pybind11_protobuf::ImportNativeProtoCasters();
  using namespace ::learning::genomics::deepvariant;  // NOLINT

  py::class_<PhasedVariant>(m, "PhasedVariant")
      .def_readwrite("position", &PhasedVariant::position)
      .def_readwrite("phase_1_bases", &PhasedVariant::phase_1_bases)
      .def_readwrite("phase_2_bases", &PhasedVariant::phase_2_bases);

  py::classh<DirectPhasing>(m, "DirectPhasing")
      .def(py::init<>())
      .def("graphviz", &DirectPhasing::GraphViz)
      .def("get_phased_variants", &DirectPhasing::GetPhasedVariants)
      .def("phase", &DirectPhasing::PhaseReadsPython, py::arg("candidates"),
           py::arg("reads"));
}