void FileRecordMgr::deleteAllMergedItemsButKey(RecordKeyList &recList) {
//if the key is also in the list, this method won't delete it.
for (RecordKeyList::const_iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) {
if (iter->value() == recList.getKey()) {
continue;
}
deleteRecord(iter->value());
}
recList.clearList();
}
unsigned long Jaccard::getTotalIntersection(RecordKeyList *recList)
{
unsigned long intersection = 0;
const Record *key = recList->getKey();
int keyStart = key->getStartPos();
int keyEnd = key->getEndPos();
int hitIdx = 0;
for (RecordKeyList::const_iterator_type iter = recList->begin(); iter != recList->end(); iter = recList->next()) {
const Record *currRec = iter->value();
int maxStart = max(currRec->getStartPos(), keyStart);
int minEnd = min(currRec->getEndPos(), keyEnd);
if (_context->getObeySplits()) {
intersection += _blockMgr->getOverlapBases(hitIdx);
hitIdx++;
} else {
intersection += (unsigned long)(minEnd - maxStart);
}
}
_numIntersections += (int)recList->size();
return intersection;
}
void BamRecord::printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyList) const
{
outBuf.append('\t');
outBuf.append(_startPosStr);
outBuf.append('\t');
outBuf.append(_endPos);
outBuf.append("\t0,0,0", 6);
outBuf.append('\t');
int numBlocks = (int)keyList->size();
if (numBlocks > 0) {
outBuf.append(numBlocks);
vector<int> blockLengths;
vector<int> blockStarts;
for (RecordKeyList::const_iterator_type iter = keyList->begin(); iter != keyList->end(); iter = keyList->next()) {
const Record *block = iter->value();
blockLengths.push_back(block->getEndPos() - block->getStartPos());
blockStarts.push_back(block->getStartPos() - _startPos);
}
outBuf.append('\t');
for (int i=0; i < (int)blockLengths.size(); i++) {
outBuf.append(blockLengths[i]);
outBuf.append(',');
}
outBuf.append('\t');
for (int i=0; i < (int)blockStarts.size(); i++) {
outBuf.append( blockStarts[i]);
outBuf.append(',');
}
}
else {
outBuf.append("1\t0,\t0,");
}
}
