diff --git a/Makefile b/Makefile
index d94a391..d248b9d 100644
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,9 @@
 BINDIR ?= $(PREFIX)/bin
 BIN = $(DESTDIR)/$(BINDIR)
 # With pthreads
-override CXXFLAGS+= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 -march=native -g
+override CXXFLAGS+= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 $(EXTRA_CXXFLAGS)
 # Without pthreads
-#override CXXFLAGS+= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 -march=native
+#override CXXFLAGS+= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 $(EXTRA_CXXFLAGS)
 
 THREAD=	-lpthread
 
@@ -14,15 +14,14 @@ all: bsmap
 %.o:%.cpp
 	$(CXX) $(CXXFLAGS) -c $< -o $@
 bsmap: $(OBJS1)
-	(cd samtools; make)
-	(cd gzstream; make)
+	$(MAKE) -C samtools
+	$(MAKE) -C gzstream
 	$(CXX) $(CXXFLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream
-	rm -f *.o
 
 clean:
 	rm -f *.o *~ bsmap
-	(cd samtools; make clean)
-	(cd gzstream; make clean)
+	$(MAKE) -C samtools clean
+	$(MAKE) -C gzstream clean
 install:
 	install -d $(BIN)
 	install ./bsmap $(BIN)