static
JumpAlignmentResult<score_t>
testAlignScores(
const std::string& seq,
const std::string& ref1,
const std::string& ref2,
int match, int mismatch, int open, int extend, int spliceOpen, int offEdge, int spliceOffEdge)
{
AlignmentScores<score_t> scores(match, mismatch, open, extend, offEdge);
score_t jumpScore(-3);
GlobalJumpIntronAligner<score_t> aligner(scores,jumpScore,spliceOpen,spliceOffEdge);
JumpAlignmentResult<score_t> result;
aligner.align(
seq.begin(),seq.end(),
ref1.begin(),ref1.end(),
ref2.begin(),ref2.end(),
false, false, //todo make tests for all ortientations
result);
return result;
}
static
JumpAlignmentResult<score_t>
testAlignScores(
const std::string& seq,
const std::string& ref1,
const std::string& ref2,
int match, int mismatch, int open, int extend, int spliceOpen, int offEdge, int spliceOffEdge, int jump,
bool stranded, bool bp1Fw, bool bp2Fw)
{
AlignmentScores<score_t> scores(match, mismatch, open, extend, offEdge);
score_t jumpScore(jump);
GlobalJumpIntronAligner<score_t> aligner(scores,jumpScore,spliceOpen,spliceOffEdge);
JumpAlignmentResult<score_t> result;
aligner.align(
seq.begin(),seq.end(),
ref1.begin(),ref1.end(),
ref2.begin(),ref2.end(),
bp1Fw, bp2Fw, stranded,
result);
return result;
}
