* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308)
* Remove CXX and CXXFLAGS, ebuild sets them
* Handle python via Gentoo's EPYTHON instead

--- a/Makefile
+++ b/Makefile
@@ -16,17 +16,9 @@
 export BIN_DIR	= bin
 export SRC_DIR	= src
 export UTIL_DIR	= src/utils
-export CXX		= g++
-ifeq ($(DEBUG),1)
-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
-else
-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
-endif
 export LIBS		= -lz
 export BT_ROOT  = src/utils/BamTools/
 
-prefix ?= /usr/local
-
 SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/bamToBed \
 		  $(SRC_DIR)/bamToFastq \
@@ -135,13 +127,13 @@
 
 all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
 	@echo "- Building main bedtools binary."
-	@$(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)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 	@echo "done."
 
 	@echo "- Creating executables for old CLI."
-	@python scripts/makeBashScripts.py
-	@chmod +x bin/*
+	$(EPYTHON) scripts/makeBashScripts.py
+	chmod +x bin/*
 	@echo "done."
 
 
--- a/src/annotateBed/Makefile
+++ b/src/annotateBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 		
 clean:
--- a/src/bamToBed/Makefile
+++ b/src/bamToBed/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)  -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/bamToFastq/Makefile
+++ b/src/bamToFastq/Makefile
@@ -24,7 +24,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/bed12ToBed6/Makefile
+++ b/src/bed12ToBed6/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/bedpeToBam/Makefile
+++ b/src/bedpeToBam/Makefile
@@ -33,7 +33,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
--- a/src/bedToBam/Makefile
+++ b/src/bedToBam/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/bedToIgv/Makefile
+++ b/src/bedToIgv/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/closestFile/Makefile
+++ b/src/closestFile/Makefile
@@ -40,7 +40,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/clusterBed/Makefile
+++ b/src/clusterBed/Makefile
@@ -25,7 +25,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/complementFile/Makefile
+++ b/src/complementFile/Makefile
@@ -42,7 +42,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/coverageFile/Makefile
+++ b/src/coverageFile/Makefile
@@ -38,7 +38,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/expand/Makefile
+++ b/src/expand/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/fastaFromBed/Makefile
+++ b/src/fastaFromBed/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/fisher/Makefile
+++ b/src/fisher/Makefile
@@ -51,7 +51,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/flankBed/Makefile
+++ b/src/flankBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 		
 clean:
 	@echo "Cleaning up."
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/getOverlap/Makefile
+++ b/src/getOverlap/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 	
 clean:
--- a/src/groupBy/Makefile
+++ b/src/groupBy/Makefile
@@ -42,7 +42,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/intersectFile/Makefile
+++ b/src/intersectFile/Makefile
@@ -39,7 +39,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/jaccard/Makefile
+++ b/src/jaccard/Makefile
@@ -43,7 +43,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/linksBed/Makefile
+++ b/src/linksBed/Makefile
@@ -25,7 +25,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/mapFile/Makefile
+++ b/src/mapFile/Makefile
@@ -38,7 +38,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/maskFastaFromBed/Makefile
+++ b/src/maskFastaFromBed/Makefile
@@ -25,7 +25,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/mergeFile/Makefile
+++ b/src/mergeFile/Makefile
@@ -40,7 +40,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/multiBamCov/Makefile
+++ b/src/multiBamCov/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/multiIntersectBed/Makefile
+++ b/src/multiIntersectBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/nekSandbox1/Makefile
+++ b/src/nekSandbox1/Makefile
@@ -35,7 +35,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/nucBed/Makefile
+++ b/src/nucBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/pairToBed/Makefile
+++ b/src/pairToBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/pairToPair/Makefile
+++ b/src/pairToPair/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 
 clean:
--- a/src/randomBed/Makefile
+++ b/src/randomBed/Makefile
@@ -23,7 +23,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/regressTest/Makefile
+++ b/src/regressTest/Makefile
@@ -24,24 +24,18 @@
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
-#OBJECTS= regressTestMain.o RegressTest.o
-#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
+OBJECTS= regressTestMain.o RegressTest.o
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= regressTest
 
-
-all: #$(BUILT_OBJECTS)
-	@echo "compiling RegressTest.cpp"
-	@$(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) $(CPPFLAGS) $(INCLUDES)
+all: $(BUILT_OBJECTS)
 	
 .PHONY: all
 
-#$(BUILT_OBJECTS): $(SOURCES)
-#	@echo "  * compiling" $(*F).cpp
-#	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-
+$(BUILT_OBJECTS): $(SOURCES)
+	@echo "  * compiling" $(*F).cpp
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/reldist/Makefile
+++ b/src/reldist/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/sampleFile/Makefile
+++ b/src/sampleFile/Makefile
@@ -37,7 +37,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/shiftBed/Makefile
+++ b/src/shiftBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/shuffleBed/Makefile
+++ b/src/shuffleBed/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/slopBed/Makefile
+++ b/src/slopBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/sortBed/Makefile
+++ b/src/sortBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/spacingFile/Makefile
+++ b/src/spacingFile/Makefile
@@ -37,7 +37,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/split/Makefile
+++ b/src/split/Makefile
@@ -25,7 +25,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/subtractFile/Makefile
+++ b/src/subtractFile/Makefile
@@ -40,7 +40,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/tagBam/Makefile
+++ b/src/tagBam/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/unionBedGraphs/Makefile
+++ b/src/unionBedGraphs/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/BamTools/Makefile
+++ b/src/utils/BamTools/Makefile
@@ -56,12 +56,12 @@
 
 $(LIBRARY): $(OBJECTS)
 	@echo " * linking $(LIBRARY)"
-	ar cr $@ $^
+	$(AR) cr $@ $^
 	-ranlib $@
 
 $(OBJECTS): $(SOURCES)
 	@echo " * compiling" $(*F).cpp
-	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp
 
 .PHONY: api
 api:
--- a/src/utils/BamTools-Ancillary/Makefile
+++ b/src/utils/BamTools-Ancillary/Makefile
@@ -21,7 +21,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/bedFile/Makefile
+++ b/src/utils/bedFile/Makefile
@@ -20,7 +20,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
--- a/src/utils/bedFilePE/Makefile
+++ b/src/utils/bedFilePE/Makefile
@@ -17,7 +17,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- a/src/utils/bedGraphFile/Makefile
+++ b/src/utils/bedGraphFile/Makefile
@@ -19,7 +19,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
--- a/src/utils/BinTree/Makefile
+++ b/src/utils/BinTree/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- a/src/utils/BlockedIntervals/Makefile
+++ b/src/utils/BlockedIntervals/Makefile
@@ -23,7 +23,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- a/src/utils/chromsweep/Makefile
+++ b/src/utils/chromsweep/Makefile
@@ -20,7 +20,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- a/src/utils/Contexts/Makefile
+++ b/src/utils/Contexts/Makefile
@@ -36,7 +36,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/driver/Makefile
+++ b/src/utils/driver/Makefile
@@ -85,7 +85,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 	
 clean:
 	@echo "Cleaning up."
--- a/src/utils/Fasta/Makefile
+++ b/src/utils/Fasta/Makefile
@@ -19,7 +19,7 @@
 	
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/FileRecordTools/FileReaders/Makefile
+++ b/src/utils/FileRecordTools/FileReaders/Makefile
@@ -32,7 +32,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/FileRecordTools/FileReaders/Makefile~
+++ b/src/utils/FileRecordTools/FileReaders/Makefile~
@@ -31,7 +31,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/FileRecordTools/Makefile
+++ b/src/utils/FileRecordTools/Makefile
@@ -34,9 +34,9 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling FileRecordMgr.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp
 	@echo "  * compiling FileRecordMergeMgr.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp
 	
 	
 
--- a/src/utils/FileRecordTools/Records/Makefile
+++ b/src/utils/FileRecordTools/Records/Makefile
@@ -37,7 +37,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/fileType/Makefile
+++ b/src/utils/fileType/Makefile
@@ -22,7 +22,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/general/Makefile
+++ b/src/utils/general/Makefile
@@ -21,7 +21,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/GenomeFile/Makefile
+++ b/src/utils/GenomeFile/Makefile
@@ -20,9 +20,9 @@
 
 $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
 	@echo "  * compiling GenomeFile.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp
 	@echo "  * compiling NewGenomeFile.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp
 
 #$(EXT_OBJECTS):
 #	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
--- a/src/utils/gzstream/Makefile
+++ b/src/utils/gzstream/Makefile
@@ -38,7 +38,7 @@
 UTILITIES_DIR = ../../utils/
 	
 ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h
-	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/KeyListOps/Makefile
+++ b/src/utils/KeyListOps/Makefile
@@ -31,7 +31,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 
 $(EXT_OBJECTS):
--- a/src/utils/NewChromsweep/Makefile
+++ b/src/utils/NewChromsweep/Makefile
@@ -34,7 +34,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/RecordOutputMgr/Makefile
+++ b/src/utils/RecordOutputMgr/Makefile
@@ -29,7 +29,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- a/src/utils/sequenceUtilities/Makefile
+++ b/src/utils/sequenceUtilities/Makefile
@@ -17,7 +17,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- a/src/utils/tabFile/Makefile
+++ b/src/utils/tabFile/Makefile
@@ -19,7 +19,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
--- a/src/utils/ToolBase/Makefile
+++ b/src/utils/ToolBase/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- a/src/utils/VectorOps/Makefile
+++ b/src/utils/VectorOps/Makefile
@@ -11,7 +11,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/utils/version/Makefile
+++ b/src/utils/version/Makefile
@@ -20,7 +20,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES) $(HEADERS)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/windowBed/Makefile
+++ b/src/windowBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/src/windowMaker/Makefile
+++ b/src/windowMaker/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/