Shortened output buffer, corrected Chromsweep errors with some print options...

Shortened output buffer, corrected Chromsweep errors with some print options due to early termination.

src/utils/FileRecordTools/RecordOutputMgr.cpp

@@ -28,14 +28,19 @@ RecordOutputMgr::RecordOutputMgr()
 : _context(NULL),
   _printable(true),
   _bamWriter(NULL),
-  _currBlockList(NULL)
+  _currBlockList(NULL),
+  _numWrites(0)
 {
 
 }
 
 RecordOutputMgr::~RecordOutputMgr()
 {
-	flush();
+	if (_outBuf.size() > 0) {
+		flush();
+		_numWrites++;
+	}
+	cerr << "Total number of buffer writes was " << _numWrites << endl;
 	if (_bamWriter != NULL) {
 		_bamWriter->Close();
 		delete _bamWriter;
@@ -105,7 +110,10 @@ RecordOutputMgr::printBamType RecordOutputMgr::printBamRecord(RecordKeyList &key
 
 void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockList)
 {
-	if (needsFlush()) flush();
+	if (needsFlush()) {
+		flush();
+		_numWrites++;
+	}
 
 	//The first time we print a record is when we print any header, because the header
 	//hasn't been read from the query file until after the first record has also been read.

src/utils/FileRecordTools/RecordOutputMgr.h

@@ -40,6 +40,7 @@ private:
 	RecordKeyList *_currBlockList;
 
 	QuickString _outBuf;
+	int _numWrites;
 
 	//some helper functions to neaten the code.
 	void tab() { _outBuf.append('\t'); }
@@ -48,7 +49,7 @@ private:
 
 	void printKey(const Record *key);
 	void printKey(const Record *key, const QuickString & start, const QuickString & end);
-	static const unsigned int MAX_OUTBUF_SIZE = 33554432; //32 Mb
+	static const unsigned int MAX_OUTBUF_SIZE = 16384; //16 K
 	bool needsFlush() const { return _outBuf.size() >= MAX_OUTBUF_SIZE *.9; }
 	void flush();
 };

src/utils/NewChromsweep/NewChromsweep.cpp

@@ -24,7 +24,8 @@ NewChromSweep::NewChromSweep(Context *context,
  	_databaseRecordsTotalLength(0),
  	_wasInitialized(false),
  	_currQueryRec(NULL),
- 	_currDatabaseRec(NULL)
+ 	_currDatabaseRec(NULL),
+ 	_runToQueryEnd(false)
 
 {
 }
@@ -52,6 +53,13 @@ bool NewChromSweep::init() {
     if (_currDatabaseRec == NULL) {
     	return false;
     }
+
+    //determine whether to stop when the database end is hit, or keep going until the
+    //end of the query file is hit as well.
+
+    if (_context->getNoHit() || _context->getWriteCount() || _context->getWriteOverlap() || _context->getWriteAllOverlap() || _context->getLeftJoin()) {
+    	_runToQueryEnd = true;
+    }
     _wasInitialized = true;
     return true;
  }
@@ -155,7 +163,7 @@ bool NewChromSweep::next(RecordKeyList &next) {
 		return false;
 	}
 
-	if (_currDatabaseRec == NULL && _cache.empty()) {
+	if (_currDatabaseRec == NULL && _cache.empty() && !_runToQueryEnd) {
 		return false;
 	}
 	_hits.clear();

src/utils/NewChromsweep/NewChromsweep.h

@@ -81,6 +81,7 @@ private:
     Record *_currDatabaseRec;
     // a cache of the current chrom from the query. used to handle chrom changes.
     QuickString _currChromName;
+    bool _runToQueryEnd;
 
     void nextRecord(bool query); //true fetches next query record, false fetches next db record.
     void nextDatabase();