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/* |
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* Copyright 2024 Google LLC. |
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* |
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* Redistribution and use in source and binary forms, with or without |
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* modification, are permitted provided that the following conditions |
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* are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright notice, |
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* this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the distribution. |
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* |
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* 3. Neither the name of the copyright holder nor the names of its |
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* contributors may be used to endorse or promote products derived from this |
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* software without specific prior written permission. |
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* |
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" |
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE |
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE |
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE |
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR |
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF |
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS |
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN |
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) |
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE |
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* POSSIBILITY OF SUCH DAMAGE. |
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*/ |
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#if true // Trick to stop tooling from moving the #include around. |
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// MUST appear before any standard headers are included. |
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#include <pybind11/pybind11.h> |
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#endif |
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#include <pybind11/stl.h> |
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#include "deepvariant/postprocess_variants.h" |
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#include "third_party/nucleus/core/python/type_caster_nucleus_status.h" |
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#include "third_party/nucleus/core/python/type_caster_nucleus_statusor.h" |
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#include "third_party/nucleus/protos/range.pb.h" |
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#include "third_party/nucleus/util/python/type_caster_nucleus_proto_ptr.h" |
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#include "pybind11_protobuf/native_proto_caster.h" |
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namespace py = pybind11; |
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PYBIND11_MODULE(postprocess_variants, m) { |
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pybind11_protobuf::ImportNativeProtoCasters(); |
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using namespace ::learning::genomics::deepvariant; // NOLINT |
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m.def("process_single_sites_tfrecords", &ProcessSingleSiteCallTfRecords, |
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py::arg("contigs"), py::arg("tfrecord_paths"), |
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py::arg("output_tfrecord_path"), py::arg("partitions")); |
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} |