bool CloseSweep::chromChange(int dbIdx, RecordKeyVector &retList, bool wantScan)
{
Record *dbRec = _currDbRecs[dbIdx];
bool haveQuery = _currQueryRec != NULL;
bool haveDB = dbRec != NULL;
if (haveQuery && _currQueryChromName != _prevQueryChromName) {
_context->testNameConventions(_currQueryRec);
testChromOrder(_currQueryRec);
}
if (haveDB) {
_context->testNameConventions(dbRec);
testChromOrder(dbRec);
}
// the files are on the same chrom
if (haveQuery && (!haveDB || _currQueryRec->sameChrom(dbRec))) {
//if this is the first time the query's chrom is ahead of the chrom that was in this cache,
//then we have to clear the cache.
if (!_caches[dbIdx].empty() && queryChromAfterDbRec(_caches[dbIdx].begin()->value())) {
clearCache(dbIdx);
clearClosestEndPos(dbIdx);
}
return false;
}
if (!haveQuery || !haveDB) return false;
if (!_caches[dbIdx].empty() && (_caches[dbIdx].begin()->value()->sameChrom(_currQueryRec))) {
//the newest DB record's chrom is ahead of the query, but the cache still
//has old records on that query's chrom
scanCache(dbIdx, retList);
finalizeSelections(dbIdx, retList);
return true;
}
// the query is ahead of the database. fast-forward the database to catch-up.
if (queryChromAfterDbRec(dbRec)) {
string oldDbChrom(dbRec->getChrName());
while (dbRec != NULL &&
queryChromAfterDbRec(dbRec)) {
_dbFRMs[dbIdx]->deleteRecord(dbRec);
if (!nextRecord(false, dbIdx)) break;
dbRec = _currDbRecs[dbIdx];
const string &newDbChrom = dbRec->getChrName();
if (newDbChrom != oldDbChrom) {
testChromOrder(dbRec);
oldDbChrom = newDbChrom;
}
}
clearCache(dbIdx);
clearClosestEndPos(dbIdx);
return false;
}
// the database is ahead of the query.
else {
// 1. scan the cache for remaining hits on the query's current chrom.
if (wantScan) scanCache(dbIdx, retList);
return true;
}
//control can't reach here, but compiler still wants a return statement.
return true;
}
Record *FileRecordMergeMgr::getNextRecord(RecordKeyVector *recList)
{
//clear the recList if there is one, and if it has records
// in it.
if (recList != NULL && !recList->allClear()) {
deleteMergedRecord(*recList);
}
_mustBeForward = _desiredStrand == SAME_STRAND_FORWARD;
_mustBeReverse = _desiredStrand == SAME_STRAND_REVERSE;
Record *startRecord = tryToTakeFromStorage();
// if we couldn't use a previously stored record for starters,
//then begin with a new one that matches strand criteria.
while (startRecord == NULL) {
startRecord = FileRecordMgr::getNextRecord();
if (startRecord == NULL) { //hit EOF!!
return NULL;
}
if ((_mustBeForward && (startRecord->getStrandVal() != Record::FORWARD)) || (_mustBeReverse && (startRecord->getStrandVal() != Record::REVERSE))) {
//record is reverse, only want forward, OR record is forward, wanted reverse
deleteRecord(startRecord);
startRecord = NULL;
continue;
}
if (startRecord->getStrandVal() == Record::UNKNOWN && _desiredStrand != ANY_STRAND) {
//there is an unknown strand, but the user specified strandedness.
deleteRecord(startRecord);
startRecord = NULL;
}
}
// OK!! We have a start record! Re-evaluate strand requirements for next recored.
_mustBeForward = _desiredStrand == SAME_STRAND_FORWARD || (_desiredStrand == SAME_STRAND_EITHER && (startRecord->getStrandVal() == Record::FORWARD));
_mustBeReverse = _desiredStrand == SAME_STRAND_REVERSE || (_desiredStrand == SAME_STRAND_EITHER && (startRecord->getStrandVal() == Record::REVERSE));
bool mustKeepOpposite = (_desiredStrand == SAME_STRAND_EITHER);
const QuickString &currChrom = startRecord->getChrName();
_foundChroms.insert(currChrom);
bool madeComposite = false;
if (recList != NULL) {
recList->push_back(startRecord);
recList->setKey(startRecord); //key of recList will just be the startRecord unless we're able to merge more.
}
Record::strandType currStrand = startRecord->getStrandVal();
bool mustMatchStrand = _desiredStrand != ANY_STRAND;
int currEnd = startRecord->getEndPos();
//now look for more records to merge with this one.
//stop when they're out of range, not on the same chromosome, or we hit EOF.
//ignore if they don't comply with strand.
Record *nextRecord = NULL;
while (nextRecord == NULL) {
bool takenFromStorage = false;
nextRecord = mustMatchStrand ? tryToTakeFromStorage(currStrand) : tryToTakeFromStorage();
if (nextRecord == NULL) {
nextRecord = FileRecordMgr::getNextRecord();
} else {
takenFromStorage = true;
}
if (nextRecord == NULL) { // EOF hit
break;
}
//delete any record from file with an unknown strand if we are doing stranded merge, but first check
//that it's chrom was the same and it's not out of range. If either is true, stop scanning.
bool mustDelete = (mustMatchStrand && nextRecord->getStrandVal() == Record::UNKNOWN);
//check that we are still on the same chromosome.
const QuickString &newChrom = nextRecord->getChrName();
if (newChrom != currChrom) { //hit a different chromosome.
//haven't seen this chromosome before, sort order is already enforced in the base class method.
if (!mustDelete) {
addToStorage(nextRecord);
} else {
deleteRecord(nextRecord);
}
nextRecord = NULL;
break;
}
//check whether it's in range
int nextStart = nextRecord->getStartPos();
if (nextStart > currEnd + _maxDistance) {
//no, it's out of range.
if (!mustDelete) {
addToStorage(nextRecord);
} else {
deleteRecord(nextRecord);
}
nextRecord = NULL;
break;
}
// NOW, going back, we can delete any unknown strand records. But don't stop scanning.
if (mustDelete) {
deleteRecord(nextRecord);
nextRecord = NULL;
continue;
}
//if taken from file, and wrong strand, store or delete.
if (!takenFromStorage && ((_mustBeForward && (nextRecord->getStrandVal() != Record::FORWARD)) || (_mustBeReverse && (nextRecord->getStrandVal() != Record::REVERSE)))) {
if (mustKeepOpposite) {
addToStorage(nextRecord);
} else {
deleteRecord(nextRecord);
}
nextRecord = NULL;
continue; //get the next record
}
//ok, they're on the same chrom and in range, and the strand is good. Do a merge.
if (recList != NULL) recList->push_back(nextRecord);
madeComposite = true;
int nextEnd = nextRecord->getEndPos();
if (nextEnd > currEnd) {
currEnd = nextEnd;
}
nextRecord = NULL;
}
if (madeComposite) {
Record *newKey = _recordMgr->allocateRecord();
(*newKey) = (*startRecord);
newKey->setEndPos(currEnd);
if (recList != NULL) recList->setKey(newKey);
_totalMergedRecordLength += currEnd - newKey->getStartPos();
return newKey;
} else {
_totalMergedRecordLength += currEnd - startRecord->getStartPos();
return startRecord;
}
// _totalMergedRecordLength += (unsigned long)(recList->getKey()->getEndPos() - recList->getKey()->getStartPos());
// return const_cast<Record *>(recList->getKey());
}
bool FileRecordMgr::allocateAndGetNextMergedRecord(RecordKeyList & recList, WANT_STRAND_TYPE desiredStrand, int maxDistance)
{
if (!recList.allClear()) {
deleteMergedRecord(recList);
}
_mustBeForward = desiredStrand == SAME_STRAND_FORWARD;
_mustBeReverse = desiredStrand == SAME_STRAND_REVERSE;
Record *startRecord = tryToTakeFromStorage();
// if we couldn't use a previously stored record for starters,
//then begin with a new one that matches strand criteria.
while (startRecord == NULL) {
startRecord = allocateAndGetNextRecord();
if (startRecord == NULL) { //hit EOF!!
return false;
}
if (_mustBeForward && !startRecord->getStrand()) {
//record is reverse, wanted forward.
addToStorage(startRecord);
startRecord = NULL;
} else if (_mustBeReverse && startRecord->getStrand()) {
//record is forward, wanted reverse
addToStorage(startRecord);
startRecord = NULL;
}
}
// OK!! We have a start record!
_mustBeForward = desiredStrand == SAME_STRAND_FORWARD || (desiredStrand == SAME_STRAND_EITHER && startRecord->getStrand());
_mustBeReverse = desiredStrand == SAME_STRAND_REVERSE || (desiredStrand == SAME_STRAND_EITHER && !startRecord->getStrand());
const QuickString &currChrom = startRecord->getChrName();
_foundChroms.insert(currChrom);
bool madeComposite = false;
recList.push_back(startRecord);
recList.setKey(startRecord); //key of recList will just be the startRecord unless we're able to merge more.
bool currStrand = startRecord->getStrand();
bool mustMatchStrand = desiredStrand != ANY_STRAND;
int currEnd = startRecord->getEndPos();
//now look for more records to merge with this one.
//stop when they're out of range, not on the same chromosome, or we hit EOF.
//ignore if they don't comply with strand.
Record *nextRecord = NULL;
while (nextRecord == NULL) {
bool takenFromStorage = false;
nextRecord = mustMatchStrand ? tryToTakeFromStorage(currStrand) : tryToTakeFromStorage();
if (nextRecord == NULL) {
nextRecord = allocateAndGetNextRecord();
} else {
takenFromStorage = true;
}
if (nextRecord == NULL) { // EOF hit
break;
}
const QuickString &newChrom = nextRecord->getChrName();
if (newChrom != currChrom) { //hit a different chromosome.
if (_foundChroms.find(newChrom) == _foundChroms.end() || takenFromStorage) {
//haven't seen this chromosome before.
addToStorage(nextRecord);
break;
} else {
//different strand, but we've already seen this chrom. File is not sorted.
fprintf(stderr, "ERROR: Input file %s is not sorted by chromosome, startPos.\n", _context->getInputFileName(_contextFileIdx).c_str());
deleteRecord(nextRecord);
deleteMergedRecord(recList);
exit(1);
}
}
int nextStart = nextRecord->getStartPos();
//is the record out of range?
if (nextStart > currEnd + maxDistance) {
//yes, it's out of range.
addToStorage(nextRecord);
break;
}
//ok, they're on the same chrom and in range. Are we happy with the strand?
if (mustMatchStrand && nextRecord->getStrand() != currStrand) {
//no, we're not.
addToStorage(nextRecord);
nextRecord = NULL;
continue;
}
//everything's good! do a merge.
recList.push_back(nextRecord);
madeComposite = true;
int nextEnd = nextRecord->getEndPos();
if (nextEnd > currEnd) {
currEnd = nextEnd;
}
nextRecord = NULL;
}
if (madeComposite) {
Record *newKey = _recordMgr->allocateRecord();
(*newKey) = (*startRecord);
newKey->setEndPos(currEnd);
recList.setKey(newKey);
}
_totalMergedRecordLength += (unsigned long)(recList.getKey()->getEndPos() - recList.getKey()->getStartPos());
return true;
}