forgot src/utils/ToolBase directory

src/utils/ToolBase/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)/RecordOutputMgr/ \
+ 			-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= ToolBase.h
+OBJECTS= ToolBase.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)/ToolBase.o 
+
+.PHONY: clean
\ No newline at end of file

src/utils/ToolBase/ToolBase.cpp

+#include "ToolBase.h"
+
+// All methods are currently purely abstract, so this file is only a placeholder for any future
+// methods that may be added.

src/utils/ToolBase/ToolBase.h

+/*
+ * ToolBase.h
+ *
+ *  Created on: Mar 25, 2015
+ *      Author: nek3d
+ */
+
+#ifndef TOOLBASE_H_
+#define TOOLBASE_H_
+
+using namespace std;
+
+#include "RecordKeyVector.h"
+#include "RecordOutputMgr.h"
+
+class ContextBase;
+
+class ToolBase {
+public:
+	ToolBase(ContextBase *context) {_context = context; }
+	virtual ~ToolBase() {}
+	virtual bool init() = 0; // after construction
+	virtual bool findNext(RecordKeyVector &hits) = 0;
+	virtual void processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) = 0;
+	virtual void cleanupHits(RecordKeyVector &hits) = 0;
+	//do any last things needed to wrap up.
+	virtual bool finalizeCalculations() = 0;
+	virtual void  giveFinalReport(RecordOutputMgr *outputMgr) = 0;
+protected:
+	ContextBase *_context;
+};
+
+
+
+#endif /* TOOLBASE_H_ */