// Convert a line from a hits file into a vector of overlaps and sets the flag
// indicating whether the read was found to be a substring of other reads
// Only the forward read table is used since we only care about the IDs and length
// of the read, not the sequence, so that we don't need an explicit reverse read table
void OverlapCommon::parseHitsString(const std::string& hitString,
const ReadInfoTable* pQueryRIT,
const ReadInfoTable* pTargetRIT,
const SuffixArray* pFwdSAI,
const SuffixArray* pRevSAI,
bool bCheckIDs,
size_t& readIdx,
size_t& sumBlockSize,
OverlapVector& outVector,
bool& isSubstring)
{
OverlapVector outvec;
std::istringstream convertor(hitString);
sumBlockSize = 0;
// Read the overlap blocks for a read
size_t numBlocks;
convertor >> readIdx >> isSubstring >> numBlocks;
//std::cout << "<Read> idx: " << readIdx << " count: " << numBlocks << "\n";
for(size_t i = 0; i < numBlocks; ++i)
{
// Read the block
OverlapBlock record;
convertor >> record;
//std::cout << "\t" << record << "\n";
// Iterate through the range and write the overlaps
for(int64_t j = record.ranges.interval[0].lower; j <= record.ranges.interval[0].upper; ++j)
{
sumBlockSize += 1;
const SuffixArray* pCurrSAI = (record.flags.isTargetRev()) ? pRevSAI : pFwdSAI;
const ReadInfo& queryInfo = pQueryRIT->getReadInfo(readIdx);
int64_t saIdx = j;
// The index of the second read is given as the position in the SuffixArray index
const ReadInfo& targetInfo = pTargetRIT->getReadInfo(pCurrSAI->get(saIdx).getID());
// Skip self alignments and non-canonical (where the query read has a lexo. higher name)
if(queryInfo.id != targetInfo.id)
{
Overlap o = record.toOverlap(queryInfo.id, targetInfo.id, queryInfo.length, targetInfo.length);
//std::cout << queryInfo.id << " " << targetInfo.id << " " << queryInfo.length << " " << targetInfo.length << "\n";
// The alignment logic above has the potential to produce duplicate alignments
// To avoid this, we skip overlaps where the id of the first coord is lexo. lower than
// the second or the match is a containment and the query is reversed (containments can be
// output up to 4 times total).
if(bCheckIDs && (o.id[0] < o.id[1] || (o.match.isContainment() && record.flags.isQueryRev())))
continue;
outVector.push_back(o);
}
}
}
}
