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 * Copyright 2024 Google LLC.

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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.

 *

 * 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

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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

 * POSSIBILITY OF SUCH DAMAGE.

 */

#include "absl/strings/string_view.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 <memory>

#include <utility>

#include "deepvariant/realigner/ssw.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(ssw, m) {

  pybind11_protobuf::ImportNativeProtoCasters();

  using namespace ::learning::genomics::deepvariant;  // NOLINT

  py::classh<Aligner>(m, "Aligner")

      .def(py::init<>())

      .def(py::init<uint8_t, uint8_t, uint8_t, uint8_t>())

      .def_static(

          "construct",

          [](uint8_t match_score, uint8_t mismatch_penalty,

             uint8_t gap_opening_penalty, uint8_t gap_extending_penalty) {

            return std::make_unique<Aligner>(std::move(match_score),

                                             std::move(mismatch_penalty),

                                             std::move(gap_opening_penalty),

                                             std::move(gap_extending_penalty));

          },

          py::arg("match_score"), py::arg("mismatch_penalty"),

          py::arg("gap_opening_penalty"), py::arg("gap_extending_penalty"))

      .def("set_reference_sequence", &Aligner::SetReferenceSequence,

           py::arg("seq"))

      .def("align", [](Aligner* self, const string& query, const Filter& filter,

                       int maskLen) {

        Alignment alignment;

        int cpp_result = self->Align(query, filter, maskLen, &alignment);

        py::object ret1 = py::cast(std::move(alignment));

        auto postproc =

            py::module_::import("third_party.nucleus.io.clif_postproc");

        py::object ret0 =

            postproc.attr("ValueErrorOnInaccurate")(cpp_result, ret1);

        return ret0;

      });

  py::classh<Filter>(m, "Filter")

      .def(py::init())

      .def(py::init<const bool&, const bool&, uint16_t, uint16_t>())

      .def_static(

          "construct",

          [](bool pos, bool cigar, uint16_t score, uint16_t dis) {

            return std::make_unique<Filter>(std::move(pos), std::move(cigar),

                                            std::move(score), std::move(dis));

          },

          py::arg("pos"), py::arg("cigar"), py::arg("int"), py::arg("dis"))

      .def_readwrite("report_begin_position", &Filter::report_begin_position)

      .def_readwrite("report_cigar", &Filter::report_cigar)

      .def_readwrite("score_filter", &Filter::score_filter)

      .def_readwrite("distance_filter", &Filter::distance_filter);

  py::classh<Alignment>(m, "Alignment")

      .def_readwrite("sw_score", &Alignment::sw_score)

      .def_readwrite("sw_score_next_best", &Alignment::sw_score_next_best)

      .def_readwrite("ref_begin", &Alignment::ref_begin)

      .def_readwrite("ref_end", &Alignment::ref_end)

      .def_readwrite("query_begin", &Alignment::query_begin)

      .def_readwrite("query_end", &Alignment::query_end)

      .def_readwrite("ref_end_next_best", &Alignment::ref_end_next_best)

      .def_readwrite("mismatches", &Alignment::mismatches)

      .def_property(

          "cigar_string",

          [](const Alignment* self) { return py::bytes(self->cigar_string); },

          [](Alignment* self, absl::string_view value) {

            self->cigar_string = value;

          });

}