@@ -27,7 +27,6 @@ DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \

   -Dabort=_samtools_abort

 PKG_CPPFLAGS += -I$(INCLUDE_DIR)

-PKG_CFLAGS += -g -O3 $(DFLAGS)

 PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz

 SHLIB = gmapR.so

@@ -39,6 +38,9 @@ $(SHLIB): $(OBJECTS) $(GSTRUCT_LIB)

 $(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c)

+samtools/%.o: samtools/%.c

+	$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(DFLAGS) -c $< -o $@

+

 $(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct

 $(SAMTOOLS_LIB): $(BAMOBJ)

@@ -69,6 +71,5 @@ clean:

 	for dir in $(SUBDIRS); do \

 	  $(MAKE) -C $$dir distclean; \

 	done

-	rm -rf samtools $(PREFIX)

 	rm -f *.o *.so *.dll