#ifndef _BLASR_SW_ALIGN_HPP_
#define _BLASR_SW_ALIGN_HPP_

template <typename T_QuerySequence, typename T_TargetSequence, typename T_Alignment,
          typename T_ScoreFn>
int SWAlign(T_QuerySequence &qSeq, T_TargetSequence &tSeq, std::vector<int> &scoreMat,
            std::vector<Arrow> &pathMat, T_Alignment &alignment, T_ScoreFn &scoreFn,
            AlignmentType alignType = Local, bool trustSequences = false, bool printMatrix = false);

#include "SWAlignImpl.hpp"

#endif  // _BLASR_SW_ALIGN_HPP_
