float
SimpleRecursor<M, E, C>::LinkAlphaBeta(const E& e,
const M& alpha, int alphaColumn,
const M& beta, int betaColumn,
int absoluteColumn) const
{
const int I = e.ReadLength();
assert(alphaColumn > 1 && absoluteColumn > 1);
assert(absoluteColumn < e.TemplateLength());
int usedBegin, usedEnd;
boost::tie(usedBegin, usedEnd) = \
RangeUnion(alpha.UsedRowRange(alphaColumn - 2),
alpha.UsedRowRange(alphaColumn - 1),
beta.UsedRowRange(betaColumn),
beta.UsedRowRange(betaColumn + 1));
float v = NEG_INF, thisMoveScore;
for (int i = usedBegin; i < usedEnd; i++)
{
if (i < I)
{
// Incorporate
thisMoveScore = alpha(i, alphaColumn - 1) +
e.Inc(i, absoluteColumn - 1) +
beta(i + 1, betaColumn);
v = C::Combine(v, thisMoveScore);
// Merge (2 possible ways):
thisMoveScore = alpha(i, alphaColumn - 2) +
e.Merge(i, absoluteColumn - 2) +
beta(i + 1, betaColumn);
v = C::Combine(v, thisMoveScore);
thisMoveScore = alpha(i, alphaColumn - 1) +
e.Merge(i, absoluteColumn - 1) +
beta(i + 1, betaColumn + 1);
v = C::Combine(v, thisMoveScore);
}
// Delete:
thisMoveScore = alpha(i, alphaColumn - 1) +
e.Del(i, absoluteColumn - 1) +
beta(i, betaColumn);
v = C::Combine(v, thisMoveScore);
}
return v;
}
INLINE_CALLEES void
EdnaCounts::DoCount(Feature<int> channelRead,
EdnaEvaluator& eval,
MutationScorer<SparseSseEdnaRecursor>& scorer,
int j1, int j2, float *results)
{
const SparseMatrix *alpha = scorer.Alpha();
const SparseMatrix *beta = scorer.Beta();
int usedBegin, usedEnd;
boost::tie(usedBegin, usedEnd) = RangeUnion(alpha->UsedRowRange(j1),
beta->UsedRowRange(j2));
for (int k = 0; k < 5; k++)
results[k] = NEG_INF;
for (int i = usedBegin; i < usedEnd; i++)
{
results[0] = detail::logAdd(results[0],
alpha->Get(i, j1) +
eval.ScoreMove(j1, j2, 0) +
beta->Get(i, j2));
}
int nRows = alpha->Rows();
int usedCap = usedEnd < nRows - 1 ? usedEnd : nRows - 1;
for (int i = usedBegin; i < usedCap; i++)
{
int readBase = channelRead[i];
results[readBase] = detail::logAdd(results[readBase],
alpha->Get(i, j1) +
eval.ScoreMove(j1, j2, readBase) +
beta->Get(i+1, j2));
}
}