Added -nobuf option, and changed flush to occur after every record if -nobuf is set.

src/utils/Contexts/Context.cpp

@@ -20,6 +20,7 @@ Context::Context()
   _showHelp(false),
   _obeySplits(false),
   _uncompressedBam(false),
+  _useBufferedOutput(true),
   _anyHit(false),
   _noHit(false),
   _writeA(false),
@@ -288,6 +289,10 @@ bool Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
             setSortedInput(true);
             markUsed(i - skipFirstArgs);
         }
+        else if(strcmp(argv[i], "-nobuf") == 0) {
+        	setUseBufferedOutput(false);
+            markUsed(i - skipFirstArgs);
+        }
         else if(strcmp(argv[i], "-header") == 0) {
             setPrintHeader(true);
             markUsed(i - skipFirstArgs);

src/utils/Contexts/Context.h

@@ -105,6 +105,9 @@ public:
 
     bool getUncompressedBam() const { return _uncompressedBam; }
     void setUncompressedBam(bool val) { _uncompressedBam = val; }
+
+    bool getUseBufferedOutput() const { return _useBufferedOutput; }
+    void setUseBufferedOutput(bool val) { _useBufferedOutput = val; }
 	//
 	// INTERSECT METOHDS
 	//
@@ -241,6 +244,7 @@ protected:
 	bool _showHelp;
     bool _obeySplits;
     bool _uncompressedBam;
+    bool _useBufferedOutput;
 
 	bool _anyHit;
     bool _noHit;

src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h

@@ -43,7 +43,7 @@ private:
 	bool _streamFinished;
 	QuickString _currScanBuffer;
 	//The minus ones in these constants are for leaving room for a null terminator after reading into buffers.
-	static const int MAIN_BUF_READ_SIZE = 2047; // 2 Kb minus 1
+	static const int MAIN_BUF_READ_SIZE = 1023; // 2 Kb minus 1
 	static const int GZIP_LINE_BUF_SIZE = 8191; // 8K
 	bool readFileChunk();
 	bool getTypeData();

src/utils/FileRecordTools/RecordOutputMgr.cpp

@@ -82,6 +82,7 @@ bool RecordOutputMgr::printKeyAndTerminate(RecordKeyList &keyList) {
 	} else if (bamCode == NOT_BAM) {
 		keyList.getKey()->print(_outBuf);
 		return false;
+
 	}
 	//otherwise, it was BAM_AS_BED, and the key was printed.
 	return false;
@@ -157,6 +158,7 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
 					tab();
 					_outBuf.append('0');
 					newline();
+					if (needsFlush()) flush();
 				}
 				else if (_context->getLeftJoin()) {
 					if (printKeyAndTerminate(keyList)) {
@@ -166,6 +168,7 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
 					tab();
 					null(false, true);
 					newline();
+					if (needsFlush()) flush();
 					_currBlockList = NULL;
 					return;
 				}
@@ -202,6 +205,7 @@ void RecordOutputMgr::checkForHeader() {
 		}
 	}
 	_context->setPrintHeader(false);
+	if (needsFlush()) flush();
 }
 
 void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record *hitRecord)
@@ -269,22 +273,26 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
 	if (!_context->getWriteA() && !_context->getWriteB() && !_context->getWriteOverlap() && !_context->getLeftJoin()) {
 		printKey(keyRecord, *startStr, *endStr);
 		newline();
+		if (needsFlush()) flush();
 	}
 	else if ((_context->getWriteA() && _context->getWriteB()) || _context->getLeftJoin()) {
 		printKey(keyRecord);
 		tab();
 		hitRecord->print(_outBuf);
 		newline();
+		if (needsFlush()) flush();
 	}
 	else if (_context->getWriteA()) {
 		printKey(keyRecord);
 		newline();
+		if (needsFlush()) flush();
 	}
 	else if (_context->getWriteB()) {
 		printKey(keyRecord, *startStr, *endStr);
 		tab();
 		hitRecord->print(_outBuf);
 		newline();
+		if (needsFlush()) flush();
 	}
 	else if (_context->getWriteOverlap()) {
 		int printOverlapBases = max(0, minEnd-maxStart);
@@ -294,6 +302,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
 		tab();
 		int2str(printOverlapBases, _outBuf, true);
 		newline();
+		if (needsFlush()) flush();
 	}
 }
 
@@ -305,6 +314,7 @@ void RecordOutputMgr::reportOverlapSummary(RecordKeyList &keyList)
 			return;
 		}
 		newline();
+		if (needsFlush()) flush();
 	} else if (_context->getWriteCount()) {
 		if (printKeyAndTerminate(keyList)) {
 			return;
@@ -312,11 +322,13 @@ void RecordOutputMgr::reportOverlapSummary(RecordKeyList &keyList)
 		tab();
 		int2str(numOverlapsFound, _outBuf, true);
 		newline();
+		if (needsFlush()) flush();
 	} else if (_context->getNoHit() && numOverlapsFound == 0) {
 		if (printKeyAndTerminate(keyList)) {
 			return;
 		}
 		newline();
+		if (needsFlush()) flush();
 	}
 }
 

src/utils/FileRecordTools/RecordOutputMgr.h

@@ -10,10 +10,10 @@
 
 using namespace std;
 
+#include "Context.h"
 #include "RecordKeyList.h"
 #include "api/BamWriter.h"
 
-class Context;
 class BlockMgr;
 
 class RecordOutputMgr {
@@ -53,7 +53,13 @@ private:
 	void reportOverlapSummary(RecordKeyList &keyList);
 
 	static const unsigned int MAX_OUTBUF_SIZE = 16384; //16 K
-	bool needsFlush() const { return _outBuf.size() >= MAX_OUTBUF_SIZE *.9; }
+
+	// If we are using buffered output, only flush the output buffer if it's least
+	// 90% full. If we're not using buffered output, flush if it's not empty
+	bool needsFlush() const {
+		return ((_context->getUseBufferedOutput() &&_outBuf.size() >= MAX_OUTBUF_SIZE *.9) ||
+				(!_context->getUseBufferedOutput() && !_outBuf.empty()));
+	}
 	void flush();
 };