Forgot RecordOutputMgr

src/utils/RecordOutputMgr/Makefile

-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
-# -------------------
-# define our includes
-# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/general/ \
-			-I$(UTILITIES_DIR)/fileType/ \
-			-I$(UTILITIES_DIR)/Contexts/ \
-			-I$(UTILITIES_DIR)/GenomeFile/ \
-           -I$(UTILITIES_DIR)/FileRecordTools/ \
-           -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-           -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
- 			-I$(UTILITIES_DIR)/KeyListOps/ \
-           -I$(UTILITIES_DIR)/BamTools/include \
-           -I$(UTILITIES_DIR)/BamTools/src/ \
-            -I$(UTILITIES_DIR)/version/
-         
-         
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= RecordOutputMgr.cpp RecordOutputMgr.h 
-OBJECTS= RecordOutputMgr.o
-_EXT_OBJECTS=
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-
-$(BUILT_OBJECTS): $(SOURCES)
-	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(INCLUDES)
-
-clean:
-	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/RecordOutputMgr.o 
-
+OBJ_DIR = ../../../obj/
+BIN_DIR = ../../../bin/
+UTILITIES_DIR = ../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/general/ \
+			-I$(UTILITIES_DIR)/fileType/ \
+			-I$(UTILITIES_DIR)/Contexts/ \
+			-I$(UTILITIES_DIR)/GenomeFile/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ 			-I$(UTILITIES_DIR)/KeyListOps/ \
+           -I$(UTILITIES_DIR)/BamTools/include \
+           -I$(UTILITIES_DIR)/BamTools/src/ \
+            -I$(UTILITIES_DIR)/version/
+         
+         
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= RecordOutputMgr.cpp RecordOutputMgr.h 
+OBJECTS= RecordOutputMgr.o
+_EXT_OBJECTS=
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+$(BUILT_OBJECTS): $(SOURCES)
+	@echo "  * compiling" $(*F).cpp
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+	@$(MAKE) --no-print-directory -C $(INCLUDES)
+
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/RecordOutputMgr.o 
+
 .PHONY: clean
\ No newline at end of file

src/utils/RecordOutputMgr/RecordOutputMgr.h

-/*
- * RecordOutputMgr.h
- *
- *  Created on: May 28, 2013
- *      Author: nek3d
- */
-
-#ifndef RECORDOUTPUTMGR_H_
-#define RECORDOUTPUTMGR_H_
-
-using namespace std;
-
-#include "ContextBase.h"
-#include "RecordKeyVector.h"
-#include "api/BamWriter.h"
-
-class BlockMgr;
-
-class RecordOutputMgr {
-public:
-	RecordOutputMgr();
-	~RecordOutputMgr();
-
-	//The init method must be called after all the input files are open.
-	void init(ContextBase *context);
-
-	void printRecord(const Record *record);
-	void printRecord(RecordKeyVector &keyList);
-	void printRecord(const Record *record, const QuickString & value);
-
-	//where necessary, pass additional information about splits through the blockMgr.
-	void setSplitInfo(const BlockMgr *blockMgr) { _splitInfo = blockMgr; }
-
-private:
-	typedef enum { NOT_BAM, BAM_AS_BAM, BAM_AS_BED} printBamType;
-
-	ContextBase *_context;
-	bool _printable;
-	BamTools::BamWriter *_bamWriter;
-	RecordKeyVector *_currBamBlockList;
-
-	QuickString _outBuf;
-
-	//
-	BlockMgr *_bamBlockMgr;
-	const BlockMgr *_splitInfo;
-	QuickString _afterVal; //to store values to be printed after record, such as column operations.
-	//some helper functions to neaten the code.
-	void tab() { _outBuf.append('\t'); }
-	void newline() { _outBuf.append('\n'); }
-	void null(bool queryType, bool dbType);
-
-	void printRecord(RecordKeyVector &keyList, RecordKeyVector *blockList);
-	void printKey(const Record *key);
-	void printKey(const Record *key, const QuickString & start, const QuickString & end);
-	void addDbFileId(int fileId);
-	bool printKeyAndTerminate(RecordKeyVector &keyList);
-	printBamType printBamRecord(RecordKeyVector &keyList, bool bamOutputOnly = false);
-	void checkForHeader();
-	void reportOverlapDetail(const Record *keyRecord, const Record *hitRecord, int hitIdx = 0);
-	void reportOverlapSummary(RecordKeyVector &keyList);
-
-	static const unsigned int MAX_OUTBUF_SIZE = 16384; //16 K
-
-	// 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();
-};
-
-#endif /* RECORDOUTPUTMGR_H_ */
+/*
+ * RecordOutputMgr.h
+ *
+ *  Created on: May 28, 2013
+ *      Author: nek3d
+ */
+
+#ifndef RECORDOUTPUTMGR_H_
+#define RECORDOUTPUTMGR_H_
+
+using namespace std;
+
+#include "ContextBase.h"
+#include "RecordKeyVector.h"
+#include "api/BamWriter.h"
+
+class BlockMgr;
+
+class RecordOutputMgr {
+public:
+	RecordOutputMgr();
+	~RecordOutputMgr();
+
+	//The init method must be called after all the input files are open.
+	void init(ContextBase *context);
+
+	void printRecord(const Record *record);
+	void printRecord(RecordKeyVector &keyList);
+	void printRecord(const Record *record, const QuickString & value);
+
+	void printClosest(RecordKeyVector &keyList, const vector<int> *dists = NULL);
+
+	//where necessary, pass additional information about splits through the blockMgr.
+	void setSplitInfo(const BlockMgr *blockMgr) { _splitInfo = blockMgr; }
+
+private:
+	typedef enum { NOT_BAM, BAM_AS_BAM, BAM_AS_BED} printBamType;
+
+	ContextBase *_context;
+	bool _printable;
+	BamTools::BamWriter *_bamWriter;
+	RecordKeyVector *_currBamBlockList;
+
+	QuickString _outBuf;
+
+	//
+	BlockMgr *_bamBlockMgr;
+	const BlockMgr *_splitInfo;
+	QuickString _afterVal; //to store values to be printed after record, such as column operations.
+	//some helper functions to neaten the code.
+	void tab() { _outBuf.append('\t'); }
+	void newline() { _outBuf.append('\n'); }
+	void null(bool queryType, bool dbType);
+
+	void printRecord(RecordKeyVector &keyList, RecordKeyVector *blockList);
+	void printKey(const Record *key);
+	void printKey(const Record *key, const QuickString & start, const QuickString & end);
+	void addDbFileId(int fileId);
+	bool printKeyAndTerminate(RecordKeyVector &keyList);
+	printBamType printBamRecord(RecordKeyVector &keyList, bool bamOutputOnly = false);
+	void checkForHeader();
+	void reportOverlapDetail(const Record *keyRecord, const Record *hitRecord, int hitIdx = 0);
+	void reportOverlapSummary(RecordKeyVector &keyList);
+
+	static const unsigned int MAX_OUTBUF_SIZE = 16384; //16 K
+
+	// 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();
+};
+
+#endif /* RECORDOUTPUTMGR_H_ */