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);
}
