/*
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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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 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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#include <memory>
#include <vector>

#include <gmock/gmock-generated-matchers.h>
#include <gmock/gmock-matchers.h>
#include <gmock/gmock-more-matchers.h>

#include "tensorflow/core/platform/test.h"
#include "third_party/nucleus/io/vcf_reader.h"
#include "third_party/nucleus/io/vcf_writer.h"
#include "third_party/nucleus/platform/types.h"
#include "third_party/nucleus/protos/variants.pb.h"
#include "third_party/nucleus/testing/protocol-buffer-matchers.h"
#include "third_party/nucleus/testing/test_utils.h"
#include "third_party/nucleus/core/status_matchers.h"

namespace nucleus {

namespace {
using genomics::v1::Variant;
}  // namespace

// Read from a vcf file and write to a bcf file. The bcf file should have the
// same contents as the vcf file.
TEST(VcfRoundtripTest, ReadVCFWriteBCF) {
  string input_file = GetTestData("test_sites.vcf");
  string output_file = MakeTempFile("output.bcf.gz");
  auto reader = std::move(
      VcfReader::FromFile(input_file, genomics::v1::VcfReaderOptions())
          .ValueOrDie());
  auto writer = std::move(VcfWriter::ToFile(output_file, reader->Header(),
                                            genomics::v1::VcfWriterOptions())
                              .ValueOrDie());
  std::vector<Variant> expected_variants = as_vector(reader->Iterate());
  for (const auto& v : expected_variants) {
    ASSERT_THAT(writer->Write(v), IsOK());
  }
  writer = nullptr;
  auto output_reader = std::move(
      VcfReader::FromFile(output_file, genomics::v1::VcfReaderOptions())
          .ValueOrDie());
  EXPECT_THAT(as_vector(output_reader->Iterate()),
              testing::Pointwise(EqualsProto(), expected_variants));
}

}  // namespace nucleus