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#include "deepvariant/postprocess_variants.h"

#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/protos/reference.pb.h"
#include "third_party/nucleus/protos/variants.pb.h"
#include "third_party/nucleus/testing/test_utils.h"

namespace learning {
namespace genomics {
namespace deepvariant {

namespace {

CallVariantsOutput CreateSingleSiteCalls(absl::string_view reference_name,
                                         int start,
                                         int end) {
  CallVariantsOutput single_site_call;
  // Add one call to fulfill the assumption of variant having one call.
  single_site_call.mutable_variant()->add_calls();
  single_site_call.mutable_variant()->set_reference_name(
      string(reference_name));
  single_site_call.mutable_variant()->set_start(start);
  single_site_call.mutable_variant()->set_end(end);
  return single_site_call;
}

CallVariantsOutput CreateSingleSiteCalls(absl::string_view reference_name,
                                         int start,
                                         int end, double quality) {
  CallVariantsOutput single_site_call =
      CreateSingleSiteCalls(reference_name, start, end);
  single_site_call.mutable_variant()->set_quality(quality);
  return single_site_call;
}

}  // namespace

TEST(ProcessSingleSiteCallTfRecords, BasicCase) {
  std::vector<nucleus::genomics::v1::ContigInfo> contigs =
      nucleus::CreateContigInfos({"chr1", "chr10"}, {0, 1000});
  std::vector<CallVariantsOutput> single_site_calls;
  single_site_calls.push_back(CreateSingleSiteCalls("chr10", 2000, 2001));
  single_site_calls.push_back(CreateSingleSiteCalls("chr10", 1000, 1001));
  single_site_calls.push_back(CreateSingleSiteCalls("chr1", 1, 2));
  single_site_calls.push_back(CreateSingleSiteCalls("chr10", 2000, 2002, 0.9));
  single_site_calls.push_back(CreateSingleSiteCalls("chr10", 2000, 2002, 0.7));
  const string& input_tfrecord_path = nucleus::MakeTempFile(
      "ProessSingleSiteCallTfRecordsBasicCase.in.tfrecord");
  const string& output_tfrecord_path = nucleus::MakeTempFile(
      "ProessSingleSiteCallTfRecordsBasicCase.out.tfrecord");
  nucleus::WriteProtosToTFRecord(single_site_calls, input_tfrecord_path);

  ProcessSingleSiteCallTfRecords(contigs, {input_tfrecord_path},
                                 output_tfrecord_path);
  std::vector<CallVariantsOutput> output =
      nucleus::ReadProtosFromTFRecord<CallVariantsOutput>(output_tfrecord_path);

  EXPECT_EQ(output.size(), 5);
  EXPECT_EQ(output[0].variant().reference_name(), "chr1");
  EXPECT_EQ(output[1].variant().reference_name(), "chr10");
  EXPECT_EQ(output[2].variant().reference_name(), "chr10");
  EXPECT_EQ(output[3].variant().reference_name(), "chr10");
  EXPECT_EQ(output[4].variant().reference_name(), "chr10");
  EXPECT_EQ(output[0].variant().start(), 1);
  EXPECT_EQ(output[1].variant().start(), 1000);
  EXPECT_EQ(output[2].variant().start(), 2000);
  EXPECT_EQ(output[3].variant().start(), 2000);
  EXPECT_EQ(output[4].variant().start(), 2000);
  EXPECT_EQ(output[0].variant().end(), 2);
  EXPECT_EQ(output[1].variant().end(), 1001);
  EXPECT_EQ(output[2].variant().end(), 2001);
  EXPECT_EQ(output[3].variant().end(), 2002);
  EXPECT_EQ(output[4].variant().end(), 2002);
  // Order of calls with the same reference, start, end should be preserved.
  EXPECT_EQ(output[3].variant().quality(), 0.9);
  EXPECT_EQ(output[4].variant().quality(), 0.7);
}

}  // namespace deepvariant
}  // namespace genomics
}  // namespace learning