/*
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 * 2. Redistributions in binary form must reproduce the above copyright
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 *    software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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#include "deepvariant/realigner/ssw.h"
#include "src/ssw_cpp.h"

namespace learning {
namespace genomics {
namespace deepvariant {

using std::string;

Filter::Filter()
    : StripedSmithWaterman::Filter()
    {}

// NOLINTNEXTLINE: const bool& is silly; just mirroring the API in superclass.
Filter::Filter(const bool& pos, const bool& cigar,
               const uint16_t& score, const uint16_t& dis)
    : StripedSmithWaterman::Filter(pos, cigar, score, dis)
    {}

Aligner::Aligner()
    : StripedSmithWaterman::Aligner()
    {}

Aligner::Aligner(const uint8_t& match_score,
                 const uint8_t& mismatch_penalty,
                 const uint8_t& gap_opening_penalty,
                 const uint8_t& gap_extending_penalty)
    : StripedSmithWaterman::Aligner(match_score, mismatch_penalty,
                                    gap_opening_penalty, gap_extending_penalty)
    {}


int Aligner::SetReferenceSequence(const string& reference) {
  return StripedSmithWaterman::Aligner::SetReferenceSequence(
      reference.c_str(), reference.length());
}

int Aligner::Align(const string& query, const Filter& filter,
                    Alignment* alignment) const {
  return StripedSmithWaterman::Aligner::Align(
      query.c_str(), filter, alignment, query.length());
}

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