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#ifndef LEARNING_GENOMICS_DEEPVARIANT_POSTPROCESS_VARIANTS_H_
#define LEARNING_GENOMICS_DEEPVARIANT_POSTPROCESS_VARIANTS_H_

#include <string>
#include <vector>

#include "deepvariant/protos/deepvariant.pb.h"
#include "third_party/nucleus/protos/reference.pb.h"

namespace learning {
namespace genomics {
namespace deepvariant {

using std::string;

// Reads TFRecord of CallVariantsOutput protos, sort them based
// on the mapping of chromosome names to positions in FASTA in `contigs`,
// and then outputs the sorted TFRecord of CallVariantsOutput protos to
// `output_tfrecord_path`.
std::uint64_t ProcessSingleSiteCallTfRecords(
    const std::vector<nucleus::genomics::v1::ContigInfo>& contigs,
    const std::vector<std::string>& tfrecord_paths,
    const string& output_tfrecord_path);

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

#endif  // LEARNING_GENOMICS_DEEPVARIANT_POSTPROCESS_VARIANTS_H_