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#include "deepvariant/realigner/ssw.h"

#include <stdio.h>

#include "absl/strings/str_format.h"
#include "src/ssw_cpp.h"
#include "tensorflow/core/platform/types.h"

namespace learning {
namespace genomics {
namespace deepvariant {

using tensorflow::string;

// This exercises a bug in gcc 5.4.  internal
// Building libssw with -fno-inline should work around it.
// Updated Oct 2022: Even though we no longer need the workaround, I'm keeping
// this test.
int Gcc54Bug() {
  Aligner a(4, 2, 4, 2);
  Filter f;
  Alignment x;
  a.SetReferenceSequence("tttt");
  bool ok = a.Align("ttAtt", f, &x);
  if (!ok) return 1;
  absl::PrintF("ok=%d cigar=%s\n", ok, x.cigar_string);
  if (x.cigar_string != "2=1I2=") return 1;
  return 0;
}

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

int main() { return learning::genomics::deepvariant::Gcc54Bug(); }
