AlphaCount64 BWTAlgorithms::calculateDeBruijnExtensionsSingleIndex(const std::string str,
const BWT* pBWT,
EdgeDir direction,
const BWTIntervalCache* pFwdCache)
{
size_t k = str.size();
size_t p = k - 1;
std::string pmer;
// In the sense direction, we extend from the 3' end
if(direction == ED_SENSE)
pmer = str.substr(1, p);
else
pmer = str.substr(0, p);
assert(pmer.length() == p);
std::string rc_pmer = reverseComplement(pmer);
// As we only have a single index, we can only directly look up
// the extensions for either the pmer or its reverse complement
// In the SENSE extension direction, we directly look up for
// the reverse complement. In ANTISENSE we directly look up for
// the pmer.
// Get the extension bases
AlphaCount64 extensions;
AlphaCount64 rc_extensions;
// Set up pointers to the data to fill in/query
// depending on the direction of the extension
AlphaCount64* pDirectEC;
AlphaCount64* pIndirectEC;
std::string* pDirectStr;
std::string* pIndirectStr;
if(direction == ED_SENSE)
{
pDirectEC = &rc_extensions;
pDirectStr = &rc_pmer;
pIndirectEC = &extensions;
pIndirectStr = &pmer;
}
else
{
pDirectEC = &extensions;
pDirectStr = &pmer;
pIndirectEC = &rc_extensions;
pIndirectStr = &rc_pmer;
}
// Get the interval for the direct query string
BWTInterval interval;
// Use interval cache if available
if(pFwdCache)
interval = BWTAlgorithms::findIntervalWithCache(pBWT, pFwdCache, *pDirectStr);
else
interval = BWTAlgorithms::findInterval(pBWT, *pDirectStr);
// Fill in the direct count
if(interval.isValid())
*pDirectEC = BWTAlgorithms::getExtCount(interval, pBWT);
// Now, for the non-direct index, query the 4 possible k-mers that are adjacent to the pmer
// Setup the query sequence
std::string query(k, 'A');
int varIdx = query.size() - 1;
query.replace(0, p, *pIndirectStr);
for(int i = 0; i < BWT_ALPHABET::size; ++i)
{
// Transform the query
char b = BWT_ALPHABET::getChar(i);
query[varIdx] = b;
// Perform lookup
if(pFwdCache)
interval = BWTAlgorithms::findIntervalWithCache(pBWT, pFwdCache, query);
else
interval = BWTAlgorithms::findInterval(pBWT, query);
// Update the extension count
if(interval.isValid())
pIndirectEC->add(b, interval.size());
}
// Switch the reverse-complement extensions to the same strand as the str
rc_extensions.complement();
extensions += rc_extensions;
return extensions;
}
