resolve conflict

Makefile

@@ -134,8 +134,8 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
 
 all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
 	@echo "- Building main bedtools binary."
-	@$(CXX) $(CXXFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-	@$(CXX) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
+	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
+	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
 	@echo "done."
 	
 	@echo "- Creating executables for old CLI."

src/annotateBed/Makefile

@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 		
 clean:

src/bamToBed/Makefile

@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) 
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
 
 clean:
 	@echo "Cleaning up."

src/bamToFastq/Makefile

@@ -24,7 +24,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) 
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
 
 clean:
 	@echo "Cleaning up."

src/bed12ToBed6/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/bedToBam/Makefile

@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/bedToIgv/Makefile

@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/bedpeToBam/Makefile

@@ -33,7 +33,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	

src/closestFile/Makefile

@@ -39,7 +39,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/clusterBed/Makefile

@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/expand/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/fastaFromBed/Makefile

@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/fisher/Makefile

@@ -51,7 +51,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/flankBed/Makefile

@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 		
 clean:
 	@echo "Cleaning up."

src/genomeCoverageBed/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/getOverlap/Makefile

@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 	
 clean:

src/groupBy/Makefile

@@ -25,7 +25,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
            -I$(UTILITIES_DIR)/version/ \
            -I$(UTILITIES_DIR)/ToolBase/ \
            -I$(TOOL_DIR)/intersectFile/
-            
+
 
 # ----------------------------------
 # define our source and object files
@@ -41,7 +41,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/intersectFile/Makefile

@@ -38,7 +38,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/jaccard/Makefile

@@ -42,7 +42,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/linksBed/Makefile

@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/mapFile/Makefile

@@ -37,7 +37,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/maskFastaFromBed/Makefile

@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/mergeFile/Makefile

@@ -39,7 +39,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/multiBamCov/Makefile

@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/multiIntersectBed/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/nekSandbox1/Makefile

@@ -35,7 +35,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/nucBed/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/pairToBed/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/pairToPair/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 
 clean:

src/randomBed/Makefile

@@ -23,7 +23,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/regressTest/Makefile

@@ -32,15 +32,15 @@ PROGRAM= regressTest
 
 all: #$(BUILT_OBJECTS)
 	@echo "compiling RegressTest.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	@echo "compiling regressTestMain.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 .PHONY: all
 
 #$(BUILT_OBJECTS): $(SOURCES)
 #	@echo "  * compiling" $(*F).cpp
-#	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+#	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 
 clean:

src/reldist/Makefile

@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/sampleFile/Makefile

@@ -36,7 +36,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/shuffleBed/Makefile

@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/slopBed/Makefile

@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/sortBed/Makefile

@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/spacingFile/Makefile

@@ -36,7 +36,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."

src/split/Makefile

@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/tagBam/Makefile

@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/unionBedGraphs/Makefile

@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/utils/BamTools-Ancillary/Makefile

@@ -21,7 +21,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
 
 clean:
 	@echo "Cleaning up."

src/utils/BamTools/Makefile

@@ -61,7 +61,7 @@ $(LIBRARY): $(OBJECTS)
 
 $(OBJECTS): $(SOURCES)
 	@echo " * compiling" $(*F).cpp
-	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
+	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
 
 .PHONY: api
 api:

src/utils/BinTree/Makefile

@@ -27,7 +27,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)

src/utils/BlockedIntervals/Makefile

@@ -23,7 +23,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)

src/utils/Contexts/Makefile

@@ -35,7 +35,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/utils/Fasta/Makefile

@@ -19,7 +19,7 @@ all: $(BUILT_OBJECTS)
 	
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
 
 clean:
 	@echo "Cleaning up."

src/utils/FileRecordTools/FileReaders/Makefile

@@ -31,7 +31,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/utils/FileRecordTools/FileReaders/Makefile~

@@ -31,7 +31,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/utils/FileRecordTools/Makefile

@@ -33,9 +33,9 @@ all: $(BUILT_OBJECTS) $(SUBDIRS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling FileRecordMgr.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	@echo "  * compiling FileRecordMergeMgr.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 	
 

src/utils/FileRecordTools/Records/Makefile

@@ -36,7 +36,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/utils/GenomeFile/Makefile

@@ -20,9 +20,9 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
 $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
 	@echo "  * compiling GenomeFile.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	@echo "  * compiling NewGenomeFile.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 #$(EXT_OBJECTS):
 #	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/

src/utils/KeyListOps/Makefile

@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 
 $(EXT_OBJECTS):

src/utils/NewChromsweep/Makefile

@@ -33,7 +33,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/utils/RecordOutputMgr/Makefile

@@ -28,7 +28,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)

src/utils/VectorOps/Makefile

@@ -11,7 +11,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."

src/utils/bedFile/Makefile

@@ -20,7 +20,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)

src/utils/bedFilePE/Makefile

@@ -17,7 +17,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))