bool CloseSweep::chromChange(int dbIdx, RecordKeyVector &retList)
{
// if (_currQueryRec->getChrName() == "chr1_gl000191_random" || (_currDbRecs[dbIdx] != NULL && _currDbRecs[dbIdx]->getChrName() == "chr1_gl000191_random")) {
// printf("Break point here.\n");
// }
// the files are on the same chrom
if (_currDbRecs[dbIdx] == NULL || _currQueryRec->sameChrom(_currDbRecs[dbIdx])) {
//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() && _currQueryRec->chromAfter(_caches[dbIdx].begin()->value())) {
clearCache(dbIdx);
_maxPrevLeftClosestEndPos[dbIdx] = 0;
}
return false;
}
if (_currDbRecs[dbIdx]->chromAfter(_currQueryRec) && (!_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 (_currQueryRec->chromAfter(_currDbRecs[dbIdx])) {
while (_currDbRecs[dbIdx] != NULL &&
_currQueryRec->chromAfter(_currDbRecs[dbIdx])) {
_dbFRMs[dbIdx]->deleteRecord(_currDbRecs[dbIdx]);
nextRecord(false, dbIdx);
}
clearCache(dbIdx);
_maxPrevLeftClosestEndPos[dbIdx] = 0;
return false;
}
// the database is ahead of the query.
else {
// 1. scan the cache for remaining hits on the query's current chrom.
scanCache(dbIdx, retList);
return true;
}
//control can't reach here, but compiler still wants a return statement.
return true;
}
void CloseSweep::masterScan(RecordKeyVector &retList) {
//first clear out everything from the previous scan
if (_context->reportDistance()) {
_finalDistances.clear();
}
//initialize distances
for (int i=0; i < _numDBs; i++) {
_minUpstreamDist[i] = INT_MAX;
_minDownstreamDist[i] = INT_MAX;
}
for (int i=0; i < _numDBs; i++) {
_minUpstreamRecs[i]->clear();
_minDownstreamRecs[i]->clear();
_overlapRecs[i]->clear();
if (dbFinished(i) || chromChange(i, retList)) {
continue;
} else {
// scan the database cache for hits
scanCache(i, retList);
// skip if we hit the end of the DB
// advance the db until we are ahead of the query. update hits and cache as necessary
bool stopScanning = false;
while (_currDbRecs[i] != NULL &&
_currQueryRec->sameChrom(_currDbRecs[i]) &&
!stopScanning) {
if (considerRecord(_currDbRecs[i], i, stopScanning) == DELETE) {
_dbFRMs[i]->deleteRecord(_currDbRecs[i]);
_currDbRecs[i] = NULL;
} else {
_caches[i].push_back(_currDbRecs[i]);
_currDbRecs[i] = NULL;
}
nextRecord(false, i);
}
}
finalizeSelections(i, retList);
}
checkMultiDbs(retList);
}
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;
}
