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// Misc. utilities used throughout DeepVariant
#ifndef LEARNING_GENOMICS_DEEPVARIANT_UTILS_H_
#define LEARNING_GENOMICS_DEEPVARIANT_UTILS_H_

#include "absl/strings/string_view.h"
#include "deepvariant/protos/deepvariant.pb.h"
#include "third_party/nucleus/protos/variants.pb.h"

namespace learning {
namespace genomics {
namespace deepvariant {

using std::string;

// Creates an allele with the provided bases, type, and count.
Allele MakeAllele(absl::string_view bases, const AlleleType type,
                  const int count, const bool is_low_quality = false);

// First simplifies ref and alt by removing the common suffix, and the returns
// simplified_ref->simplified_alt.
string SimplifyRefAlt(absl::string_view ref, absl::string_view alt);

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

#endif  // LEARNING_GENOMICS_DEEPVARIANT_UTILS_H_