// Count the number of occurrences of string w, including the reverse complement using a BWTInterval cache
size_t BWTAlgorithms::countSequenceOccurrencesWithCache(const std::string& w, const BWT* pBWT, const BWTIntervalCache* pIntervalCache)
{
BWTInterval fwd_interval = findIntervalWithCache(pBWT, pIntervalCache, w);
BWTInterval rc_interval = findIntervalWithCache(pBWT, pIntervalCache, reverseComplement(w));
size_t count = 0;
if(fwd_interval.isValid())
count += fwd_interval.size();
if(rc_interval.isValid())
count += rc_interval.size();
return count;
}
// Delegate the findInterval call based on what indices are loaded
BWTInterval BWTAlgorithms::findInterval(const BWTIndexSet& indices, const std::string& w)
{
if(indices.pCache != NULL)
return findIntervalWithCache(indices.pBWT, indices.pCache, w);
else
return findInterval(indices.pBWT, w);
}
size_t BWTAlgorithms::countSequenceOccurrencesSingleStrand(const std::string& w, const BWTIndexSet& indices)
{
assert(indices.pBWT != NULL);
assert(indices.pCache != NULL);
BWTInterval interval = findIntervalWithCache(indices.pBWT, indices.pCache, w);
return interval.isValid() ? interval.size() : 0;
}