static JumpAlignmentResult<score_t> testAlignSplice( const std::string& seq, const std::string& ref1, const std::string& ref2) { return testAlignScores(seq, ref1, ref2, 2,-4,-5,-1,-4,-1,-1); }
static JumpAlignmentResult<score_t> testAlign( const std::string& seq, const std::string& ref1, const std::string& ref2) { AlignmentScores<score_t> scores(2, -4, -5, -1, -1); return testAlignScores(seq, ref1, ref2, 2, -4, -5, -1, -4, -1, -1, -3, true, true, true); }
static JumpAlignmentResult<score_t> testAlignSpliceNoJump( const std::string& seq, const std::string& ref1, const std::string& ref2, bool stranded = true, bool fw = true) { return testAlignScores(seq, ref1, ref2, 2, -8, -19, -1, -15, -1, -1, -10000, stranded, fw, fw); }