void BlockMgr::getBlocksFromBed12(RecordKeyVector &keyList, bool &mustDelete)
{
const Bed12Interval *keyRecord = static_cast<const Bed12Interval *>(keyList.getKey());
int blockCount = keyRecord->getBlockCount();
if ( blockCount <= 0 ) {
mustDelete = false;
return;
}
int sizeCount = _blockSizeTokens.tokenize(keyRecord->getBlockSizes(), ',');
int startCount = _blockStartTokens.tokenize(keyRecord->getBlockStarts(), ',');
if (blockCount != sizeCount || sizeCount != startCount) {
fprintf(stderr, "Error: found wrong block counts while splitting entry.\n");
exit(-1);
}
for (int i=0; i < blockCount; i++) {
int startPos = keyRecord->getStartPos() + str2chrPos(_blockStartTokens.getElem(i).c_str());
int endPos = startPos + str2chrPos(_blockSizeTokens.getElem(i).c_str());
Record *record = allocateAndAssignRecord(keyRecord, startPos, endPos);
keyList.push_back(record);
}
mustDelete = true;
}
void BlockMgr::getBlocksFromBam(RecordKeyVector &keyList, bool &mustDelete)
{
const BamRecord *keyRecord = static_cast<const BamRecord *>(keyList.getKey());
const vector<BamTools::CigarOp> &cigarData = keyRecord->getCigarData();
int currPos = keyRecord->getStartPos();
int blockLength = 0;
for (int i=0; i < (int)cigarData.size(); i++) {
char opType = cigarData[i].Type;
int opLen = (int)(cigarData[i].Length);
switch(opType) {
case 'I':
case 'S':
case 'P':
case 'H':
break;
case 'M': case 'X': case '=':
blockLength += opLen;
break;
case 'D':
case 'N' :
if ((opType == 'D' && !_breakOnDeletionOps) ||
(opType == 'N' && !_breakOnSkipOps)) {
blockLength += opLen;
} else {
keyList.push_back(allocateAndAssignRecord(keyRecord, currPos, currPos + blockLength));
currPos += opLen + blockLength;
blockLength = 0;
}
break;
default:
fprintf(stderr, "ERROR: Found invalid Cigar operation: %c.\n", opType);
exit(1);
break;
}
}
if (blockLength > 0) {
keyList.push_back(allocateAndAssignRecord(keyRecord, currPos, currPos + blockLength));
}
mustDelete = true;
}
int BlockMgr::findBlockedOverlaps(RecordKeyVector &keyList, RecordKeyVector &hitList,
RecordKeyVector &resultList, RecordKeyVector *overlapList)
{
bool deleteKeyBlocks = false;
if (keyList.empty()) {
//get all the blocks for the query record, put them in it's list.
getBlocks(keyList, deleteKeyBlocks);
}
_overlapBases.clear();
int keyBlocksSumLength = getTotalBlockLength(keyList);
//Loop through every database record the query intersected with
RecordKeyVector::iterator_type hitListIter = hitList.begin();
for (; hitListIter != hitList.end(); hitListIter = hitList.next())
{
RecordKeyVector hitBlocks(*hitListIter);
bool deleteHitBlocks = false;
getBlocks(hitBlocks, deleteHitBlocks); //get all blocks for the hit record.
int hitBlockSumLength = getTotalBlockLength(hitBlocks); //get total length of the bocks for the hitRecord.
int totalHitOverlap = 0;
bool hitHasOverlap = false;
//loop through every block of the database record.
RecordKeyVector::iterator_type hitBlockIter = hitBlocks.begin();
for (; hitBlockIter != hitBlocks.end(); hitBlockIter = hitBlocks.next())
{
//loop through every block of the query record.
RecordKeyVector::iterator_type keyListIter = keyList.begin();
for (; keyListIter != keyList.end(); keyListIter = keyList.next())
{
const Record *keyBlock = *keyListIter;
const Record *hitBlock = *hitBlockIter;
int maxStart = max(keyBlock->getStartPos(), hitBlock->getStartPos());
int minEnd = min(keyBlock->getEndPos(), hitBlock->getEndPos());
int overlap = minEnd - maxStart;
if (overlap > 0) {
hitHasOverlap = true;
if (overlapList != NULL) {
overlapList->push_back(allocateAndAssignRecord(keyList.getKey(), maxStart, minEnd));
}
totalHitOverlap += overlap;
}
}
}
if (hitHasOverlap) {
if ((float) totalHitOverlap / (float)keyBlocksSumLength >= _overlapFraction) {
if (_hasReciprocal &&
((float)totalHitOverlap / (float)hitBlockSumLength >= _overlapFraction)) {
_overlapBases.push_back(totalHitOverlap);
resultList.push_back(*hitListIter);
} else if (!_hasReciprocal) {
_overlapBases.push_back(totalHitOverlap);
resultList.push_back(*hitListIter);
}
}
}
if (deleteHitBlocks) {
deleteBlocks(hitBlocks);
}
}
if (deleteKeyBlocks) {
deleteBlocks(keyList);
}
resultList.setKey(keyList.getKey());
return (int)resultList.size();
}
