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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,
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 * 2. Redistributions in binary form must reproduce the above copyright
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 *    software without specific prior written permission.
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#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/realigner/debruijn_graph.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(debruijn_graph, m) {
  pybind11_protobuf::ImportNativeProtoCasters();
  using namespace ::learning::genomics::deepvariant;  // NOLINT
  py::classh<DeBruijnGraph>(m, "DeBruijnGraph")
      .def("graphviz", &DeBruijnGraph::GraphViz)
      .def("candidate_haplotypes", &DeBruijnGraph::CandidateHaplotypes)
      .def_property_readonly("kmer_size", &DeBruijnGraph::KmerSize);
  m.def("build", &DeBruijnGraph::Build, py::arg("ref"), py::arg("reads"),
        py::arg("options"));
}