/usr/include/blasr/algorithms/alignment/SWAlign.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | #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_
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