fixing merge errors, again.

src/utils/NewChromsweep/NewChromsweep.cpp

@@ -91,11 +91,7 @@ NewChromSweep::~NewChromSweep(void) {
 }
 
 
-<<<<<<< HEAD
 void NewChromSweep::scanCache(int dbIdx, RecordKeyVector &retList) {
-=======
-void NewChromSweep::scanCache(int dbIdx) {
->>>>>>> 57ed945c121a6e7d1ea803f19bca10c25b5eff4d
 	recListIterType cacheIter = _caches[dbIdx].begin();
     while (cacheIter != _caches[dbIdx].end())
     {
@@ -119,7 +115,6 @@ void NewChromSweep::clearCache(int dbIdx)
 	recListType &cache = _caches[dbIdx];
 	for (recListIterType iter = cache.begin(); iter != cache.end(); iter = cache.next()) {
 		_dbFRMs[dbIdx]->deleteRecord(iter->value());
-<<<<<<< HEAD
 	}
 	cache.clear();
 }
@@ -154,41 +149,6 @@ void NewChromSweep::masterScan(RecordKeyVector &retList) {
 }
 
 bool NewChromSweep::chromChange(int dbIdx, RecordKeyVector &retList)
-=======
-	}
-	cache.clear();
-}
-
-void NewChromSweep::masterScan() {
-	for (int i=0; i < _numDBs; i++) {
-		if (dbFinished(i) || chromChange(i)) {
-			continue;
-		} else {
-
-			// scan the database cache for hits
-			scanCache(i);
-			//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
-			while (_currDbRecs[i] != NULL &&
-					_currQueryRec->sameChrom(_currDbRecs[i]) &&
-					!(_currDbRecs[i]->after(_currQueryRec))) {
-				if (intersects(_currQueryRec, _currDbRecs[i])) {
-					_hits.push_back(_currDbRecs[i]);
-				}
-				if (_currQueryRec->after(_currDbRecs[i])) {
-					_dbFRMs[i]->deleteRecord(_currDbRecs[i]);
-					_currDbRecs[i] = NULL;
-				} else {
-					_caches[i].push_back(_currDbRecs[i]);
-					_currDbRecs[i] = NULL;
-				}
-				nextRecord(false, i);
-			}
-		}
-	}
-}
-
-bool NewChromSweep::chromChange(int dbIdx)
 {
     // the files are on the same chrom
 	if (_currDbRecs[dbIdx] == NULL || _currQueryRec->sameChrom(_currDbRecs[dbIdx])) {
@@ -217,6 +177,7 @@ bool NewChromSweep::chromChange(int dbIdx)
 	return true;
 }
 
+
 bool NewChromSweep::next(RecordKeyVector &retList) {
 	retList.clearVector();
 	if (_currQueryRec != NULL) {
@@ -225,19 +186,10 @@ bool NewChromSweep::next(RecordKeyVector &retList) {
 
 	if (!nextRecord(true)) return false; // query EOF hit
 
-//	QuickString outBuf;
-//	if (_currQueryRec->getStartPosStr() == "30758914") {
-//		return false;
-//	}
-//	else {
-//		_currQueryRec->print(outBuf);
-//		cerr << outBuf << endl;
-//	}
 
 	if (allCurrDBrecsNull() && allCachesEmpty() && !_runToQueryEnd) {
 		return false;
 	}
-//	_hits.clear();
 	_currChromName = _currQueryRec->getChrName();
 
 	masterScan(retList);
@@ -247,7 +199,6 @@ bool NewChromSweep::next(RecordKeyVector &retList) {
 	}
 
 	retList.setKey(_currQueryRec);
-//	retList.setListNoCopy(_hits);
 	return true;
 }
 

src/utils/NewChromsweep/NewChromsweep.h

@@ -91,11 +91,6 @@ private:
     void clearCache(int dbIdx);
     bool chromChange(int dbIdx, RecordKeyVector &retList);
 
-    bool nextRecord(bool query, int dbIdx = -1); //true fetches next query record, false fetches next db record.
-    
-    void scanCache(int dbIdx);
-    void clearCache(int dbIdx);
-    bool chromChange(int dbIdx);
     bool dbFinished(int dbIdx);
 
     bool intersects(const Record *rec1, const Record *rec2) const;