diff --git a/Makefile b/Makefile
index 46b3b3b..b1e86c1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,12 +1,11 @@
-CPPFLAGS= -DHAVE_KALLOC -fopenmp -std=c++11 -Wno-sign-compare -Wno-write-strings -Wno-unused-but-set-variable
-CFLAGS= -g -Wall -O2 #-Wextra
-LIBS= -lm -lz -lpthread
+export CPPFLAGS= -g -Wall -O2 -DHAVE_KALLOC -fopenmp -std=c++11 -Wno-sign-compare -Wno-write-strings -Wno-unused-but-set-variable
+export LIBS= -lm -lz -lpthread
 
 all:winnowmap
 
 winnowmap: MAKE_DIRS
-	+$(MAKE) -C src
-	$(CXX) $(CPPFLAGS) src/main.o -o bin/$@ -Lsrc -lwinnowmap $(LIBS)
+	+$(MAKE) -e -C src
+	$(CXX) $(CPPFLAGS)  src/main.o -o bin/$@ -Lsrc -lwinnowmap $(LIBS)
 	+$(MAKE) -C ext/meryl/src TARGET_DIR=$(shell pwd)
 
 MAKE_DIRS:
diff --git a/src/Makefile b/src/Makefile
index 49ecd32..729cee2 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -12,19 +12,19 @@ else				# if arm_neon is defined
 	OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
     INCLUDES+=-Isse2neon
 ifeq ($(aarch64),)	#if aarch64 is not defined
-	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
+	CPPFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
 else				#if aarch64 is defined
-	CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
+	CPPFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
 endif
 endif
 
 ifneq ($(asan),)
-	CFLAGS+=-fsanitize=address
+	CPPFLAGS+=-fsanitize=address
 	LIBS+=-fsanitize=address
 endif
 
 ifneq ($(tsan),)
-	CFLAGS+=-fsanitize=thread
+	CPPFLAGS+=-fsanitize=thread
 	LIBS+=-fsanitize=thread
 endif
 
@@ -32,7 +32,7 @@ endif
 .SUFFIXES:.c .o
 
 .c.o:
-		$(CXX) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+		$(CXX) -c  $(CPPFLAGS) $(INCLUDES) $< -o $@
 
 all:$(PROG)
 
@@ -42,46 +42,46 @@ libwinnowmap.a:$(OBJS)
 		$(AR) -csru $@ $(OBJS)
 
 sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
-		$(CXX) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+		$(CXX) -D_SDUST_MAIN  $< kalloc.o -o $@ -lz
 
 # SSE-specific targets on x86/x86_64
 
 ifeq ($(arm_neon),)   # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)
 ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
 endif
 
 ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
-		$(CXX) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CXX) -c  -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 # NEON-specific targets on ARM
 
 ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CXX) -c  $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
 
 ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CXX) -c  $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
 
 ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CXX) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CXX) -c  $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
 
 # other non-file targets
 
@@ -89,7 +89,7 @@ clean:
 		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
 
 depend:
-		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
+		(LC_ALL=C; export LC_ALL; makedepend -Y --  $(CPPFLAGS) -- *.c)
 
 # DO NOT DELETE