Long Read Giraffe

Makefile

@@ -5,13 +5,19 @@ CONFIG_SRC_DIR:=$(SRC_DIR)/config
 IO_SRC_DIR:=$(SRC_DIR)/io
 SUBCOMMAND_SRC_DIR:=$(SRC_DIR)/subcommand
 UNITTEST_SRC_DIR:=$(SRC_DIR)/unittest
+UNITTEST_SUPPORT_SRC_DIR:=$(SRC_DIR)/unittest/support
 BIN_DIR:=bin
+UNITTEST_BIN_DIR:=$(BIN_DIR)/unittest
 OBJ_DIR:=obj
+SHARED_OBJ_DIR:=obj/pic
 ALGORITHMS_OBJ_DIR:=$(OBJ_DIR)/algorithms
+ALGORITHMS_SHARED_OBJ_DIR:=$(SHARED_OBJ_DIR)/algorithms
 CONFIG_OBJ_DIR:=$(OBJ_DIR)/config
 IO_OBJ_DIR:=$(OBJ_DIR)/io
+IO_SHARED_OBJ_DIR:=$(SHARED_OBJ_DIR)/io
 SUBCOMMAND_OBJ_DIR:=$(OBJ_DIR)/subcommand
 UNITTEST_OBJ_DIR:=$(OBJ_DIR)/unittest
+UNITTEST_SUPPORT_OBJ_DIR:=$(OBJ_DIR)/unittest/support
 LIB_DIR:=lib
 # INC_DIR must be a relative path
 INC_DIR:=include
@@ -26,11 +32,15 @@ all: $(BIN_DIR)/$(EXE)
 
 # Magic dependencies (see <http://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#tldr>)
 include $(wildcard $(OBJ_DIR)/*.d)
+include $(wildcard $(SHARED_OBJ_DIR)/*.d)
 include $(wildcard $(ALGORITHMS_OBJ_DIR)/*.d)
+include $(wildcard $(ALGORITHMS_SHARED_OBJ_DIR)/*.d)
 include $(wildcard $(CONFIG_OBJ_DIR)/*.d)
 include $(wildcard $(IO_OBJ_DIR)/*.d)
+include $(wildcard $(IO_SHARED_OBJ_DIR)/*.d)
 include $(wildcard $(SUBCOMMAND_OBJ_DIR)/*.d)
 include $(wildcard $(UNITTEST_OBJ_DIR)/*.d)
+include $(wildcard $(UNITTEST_BIN_DIR)/*.d)
 
 # What pkg-config-controlled system dependencies should we use compile and link flags from?
 # Use PKG_CONFIG_PATH to point the build system at the right versions of these, if they aren't picked up automatically.
@@ -52,11 +62,11 @@ DEPGEN_FLAGS := -MMD -MP
 # necessary on all platforms and suppresses warnings.
 # Also, pkg-config flags need to be made -isystem if our dependency install
 # directory is, or they might put a system HTSlib before ours.
-INCLUDE_FLAGS :=-I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | sed 's/ -I/ -isystem /g')
+INCLUDE_FLAGS :=-I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | sed 's/ -I/ -isystem /g')
 
 # Define libraries to link against.
 LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
-LD_LIB_FLAGS := $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph
+LD_LIB_FLAGS := -lvgio -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph
 # We omit Boost Program Options for now; we find it in a platform-dependent way.
 # By default it has no suffix
 BOOST_SUFFIX=""
@@ -238,9 +248,11 @@ STATIC_FLAGS=-static -static-libstdc++ -static-libgcc -Wl,--allow-multiple-defin
 
 # These are put into libvg. Grab everything except main
 OBJ = $(filter-out $(OBJ_DIR)/main.o,$(patsubst $(SRC_DIR)/%.cpp,$(OBJ_DIR)/%.o,$(wildcard $(SRC_DIR)/*.cpp)))
+SHARED_OBJ = $(patsubst $(OBJ_DIR)/%.o,$(SHARED_OBJ_DIR)/%.o,$(OBJ))
 
 # And all the algorithms
 ALGORITHMS_OBJ = $(patsubst $(ALGORITHMS_SRC_DIR)/%.cpp,$(ALGORITHMS_OBJ_DIR)/%.o,$(wildcard $(ALGORITHMS_SRC_DIR)/*.cpp))
+ALGORITHMS_SHARED_OBJ = $(patsubst $(ALGORITHMS_OBJ_DIR)/%.o,$(ALGORITHMS_SHARED_OBJ_DIR)/%.o,$(ALGORITHMS_OBJ))
 
 # These aren't put into libvg. They are linked into vg itself to communicate
 # things about the platform.
@@ -249,13 +261,20 @@ CONFIG_OBJ =
 
 # But always build all the IO logic
 IO_OBJ = $(patsubst $(IO_SRC_DIR)/%.cpp,$(IO_OBJ_DIR)/%.o,$(wildcard $(IO_SRC_DIR)/*.cpp))
+IO_SHARED_OBJ = $(patsubst $(IO_OBJ_DIR)/%.o,$(IO_SHARED_OBJ_DIR)/%.o,$(IO_OBJ))
 
 # These aren't put into libvg, but they provide subcommand implementations for the vg bianry
 SUBCOMMAND_OBJ = $(patsubst $(SUBCOMMAND_SRC_DIR)/%.cpp,$(SUBCOMMAND_OBJ_DIR)/%.o,$(wildcard $(SUBCOMMAND_SRC_DIR)/*.cpp))
 
 # These aren't put into libvg. But they do go into the main vg binary to power its self-test.
 UNITTEST_OBJ = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_OBJ_DIR)/%.o,$(wildcard $(UNITTEST_SRC_DIR)/*.cpp))
 
+# These support the tests. Some should go into the main vg binary but some should only go into test-suite binaries.
+UNITTEST_SUPPORT_OBJ = $(patsubst $(UNITTEST_SUPPORT_SRC_DIR)/%.cpp,$(UNITTEST_SUPPORT_OBJ_DIR)/%.o,$(wildcard $(UNITTEST_SUPPORT_SRC_DIR)/*.cpp))
+
+# These are per-test-suite binaries we can build faster
+UNITTEST_EXE = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_BIN_DIR)/%,$(wildcard $(UNITTEST_SRC_DIR)/*.cpp))
+
 
 RAPTOR_DIR:=deps/raptor
 JEMALLOC_DIR:=deps/jemalloc
@@ -299,7 +318,7 @@ DEP_OBJ =
 DEP_OBJ += $(OBJ_DIR)/progress_bar.o
 DEP_OBJ += $(OBJ_DIR)/sha1.o
 DEP_OBJ += $(OBJ_DIR)/Fasta.o
-
+DEP_SHARED_OBJ = $(patsubst $(OBJ_DIR)/%.o,$(SHARED_OBJ_DIR)/%.o,$(DEP_OBJ))
 
 # These are libraries that we need to build before we link vg.
 # It would be nice to dump their contents into libvg to make it stand-alone.
@@ -385,6 +404,7 @@ DEPS += $(INC_DIR)/atomic_queue.h
 
 # Aggregate all libvg deps, and exe deps other than libvg
 LIBVG_DEPS = $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ) $(DEPS)
+LIBVG_SHARED_DEPS = $(SHARED_OBJ) $(ALGORITHMS_SHARED_OBJ) $(IO_SHARED_OBJ) $(DEP_SHARED_OBJ) $(DEPS)
 EXE_DEPS = $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(DEPS) $(LINK_DEPS)
 
 # We have a target we can build to do everything but link the library and executable
@@ -393,6 +413,14 @@ objs: $(LIBVG_DEPS) $(EXE_DEPS)
 $(LIB_DIR)/libvg.a: $(LIBVG_DEPS)
 	rm -f $@
 	ar rs $@ $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ)
+
+$(LIB_DIR)/libvg.$(SHARED_SUFFIX): $(LIBVG_SHARED_DEPS)
+	rm -f $@
+	$(CXX) -shared -o $@ $(SHARED_OBJ) $(ALGORITHMS_SHARED_OBJ) $(IO_SHARED_OBJ) $(DEP_SHARED_OBJ)
+
+# Each test set can have its own binary
+$(UNITTEST_EXE): $(UNITTEST_BIN_DIR)/%: $(UNITTEST_OBJ_DIR)/%.o $(UNITTEST_SUPPORT_OBJ) $(CONFIG_OBJ) $(LIB_DIR)/libvg.$(SHARED_SUFFIX) 
+	. ./source_me.sh && $(CXX) $(LDFLAGS) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(UNITTEST_SUPPORT_OBJ) $(CONFIG_OBJ) $(LIB_DIR)/libvg.$(SHARED_SUFFIX) $(LD_LIB_DIR_FLAGS) $(LD_LIB_FLAGS) $(LD_STATIC_LIB_FLAGS) $(LD_STATIC_LIB_DEPS) 
 
 # For a normal dynamic build we remove the static build marker
 $(BIN_DIR)/$(EXE): $(LIB_DIR)/libvg.a $(EXE_DEPS)
@@ -431,7 +459,7 @@ test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BI
 	. ./source_me.sh && doc/test-docs.sh
 	cd test && rm -rf tmp && mkdir tmp && mv 2_2.mat build_graph.cpp default.mat tmp && rm -f *.* && mv tmp/* . && rmdir tmp
 
-docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp
+docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(ALGORITHMS_SRC_DIR)/*.cpp $(ALGORITHMS_SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp $(UNITTEST_SUPPORT_SRC_DIR)/*.cpp
 	doxygen
 	echo "View documentation at: file://$(PWD)/doc/doxygen/index.html"
 
@@ -505,12 +533,18 @@ $(INC_DIR)/BooPHF.h: $(BBHASH_DIR)/BooPHF.h
 $(INC_DIR)/progress_bar.hpp: $(PROGRESS_BAR_DIR)/progress_bar.hpp
 	+cp $(PROGRESS_BAR_DIR)/progress_bar.hpp $(CWD)/$(INC_DIR)
 
-$(OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/*.hpp $(PROGRESS_BAR_DIR)/*.cpp
-	+. ./source_me.sh && cd $(PROGRESS_BAR_DIR) && $(MAKE) $(FILTER) && cp progress_bar.o $(CWD)/$(OBJ_DIR)
+$(OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/progress_bar.cpp $(PROGRESS_BAR_DIR)/*.hpp
+	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $<
+$(SHARED_OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/progress_bar.cpp $(PROGRESS_BAR_DIR)/*.hpp
+	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
 
-# We also run the fastahack build process in another rule, which we need to depend on to avoid races
-$(OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/fastahack
-	+. ./source_me.sh && cd $(FASTAHACK_DIR) && $(MAKE) $(FILTER) && cp Fasta.o $(CWD)/$(OBJ_DIR) && cp Fasta.h $(CWD)/$(INC_DIR)
+$(INC_DIR)/Fasta.h:  $(FASTAHACK_DIR)/Fasta.h
+	+. ./source_me.sh && cd $(FASTAHACK_DIR) && cp Fasta.h $(CWD)/$(INC_DIR)
+
+$(OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h $(FASTAHACK_DIR)/fastahack
+	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
+$(SHARED_OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h $(FASTAHACK_DIR)/fastahack
+	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
 
 # We have this target to clean up the old Protobuf we used to have.
 # We can remove it after we no longer care about building properly on a dirty
@@ -692,6 +726,8 @@ $(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/libebl/*.c $(ELFUTILS_DIR)/libebl/*.h $(ELF
 
 $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
 	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
+$(SHARED_OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
+	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
 
 $(LIB_DIR)/libfml.a: $(FERMI_DIR)/*.h $(FERMI_DIR)/*.c
 	. ./source_me.sh && cd $(FERMI_DIR) && $(MAKE) $(FILTER) && cp *.h $(CWD)/$(INC_DIR)/ && cp libfml.a $(CWD)/$(LIB_DIR)/
@@ -786,18 +822,30 @@ $(OBJ_DIR)/version.o: $(SRC_DIR)/version.cpp $(SRC_DIR)/version.hpp $(INC_DIR)/v
 $(OBJ) $(OBJ_DIR)/main.o: $(OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp $(OBJ_DIR)/%.d $(DEPS)
 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
+$(SHARED_OBJ): $(SHARED_OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp $(SHARED_OBJ_DIR)/%.d $(DEPS)
+	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
+	@touch $@
 $(ALGORITHMS_OBJ): $(ALGORITHMS_OBJ_DIR)/%.o : $(ALGORITHMS_SRC_DIR)/%.cpp $(ALGORITHMS_OBJ_DIR)/%.d $(DEPS)
 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
+$(ALGORITHMS_SHARED_OBJ): $(ALGORITHMS_SHARED_OBJ_DIR)/%.o : $(ALGORITHMS_SRC_DIR)/%.cpp $(ALGORITHMS_SHARED_OBJ_DIR)/%.d $(DEPS)
+	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
+	@touch $@
 $(IO_OBJ): $(IO_OBJ_DIR)/%.o : $(IO_SRC_DIR)/%.cpp $(IO_OBJ_DIR)/%.d $(DEPS)
 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
+$(IO_SHARED_OBJ): $(IO_SHARED_OBJ_DIR)/%.o : $(IO_SRC_DIR)/%.cpp $(IO_SHARED_OBJ_DIR)/%.d $(DEPS)
+	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
+	@touch $@
 $(SUBCOMMAND_OBJ): $(SUBCOMMAND_OBJ_DIR)/%.o : $(SUBCOMMAND_SRC_DIR)/%.cpp $(SUBCOMMAND_OBJ_DIR)/%.d $(DEPS)
 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(UNITTEST_OBJ): $(UNITTEST_OBJ_DIR)/%.o : $(UNITTEST_SRC_DIR)/%.cpp $(UNITTEST_OBJ_DIR)/%.d $(DEPS)
 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
+$(UNITTEST_SUPPORT_OBJ): $(UNITTEST_SUPPORT_OBJ_DIR)/%.o : $(UNITTEST_SUPPORT_SRC_DIR)/%.cpp $(UNITTEST_SUPPORT_OBJ_DIR)/%.d $(DEPS)
+	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	@touch $@
 
 # Config objects get individual rules
 $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.d $(DEPS) $(LIB_DIR)/libjemalloc.a
@@ -830,13 +878,18 @@ $(UNITTEST_OBJ_DIR)/%.d: ;
 .pre-build:
 	@protoc --version >/dev/null 2>/dev/null || (echo "Error: protobuf compiler (protoc) not available!" ; exit 1)
 	@if [ ! -d $(BIN_DIR) ]; then mkdir -p $(BIN_DIR); fi
+	@if [ ! -d $(UNITTEST_BIN_DIR) ]; then mkdir -p $(UNITTEST_BIN_DIR); fi
 	@if [ ! -d $(LIB_DIR) ]; then mkdir -p $(LIB_DIR); fi
 	@if [ ! -d $(OBJ_DIR) ]; then mkdir -p $(OBJ_DIR); fi
+	@if [ ! -d $(SHARED_OBJ_DIR) ]; then mkdir -p $(SHARED_OBJ_DIR); fi
 	@if [ ! -d $(ALGORITHMS_OBJ_DIR) ]; then mkdir -p $(ALGORITHMS_OBJ_DIR); fi
+	@if [ ! -d $(ALGORITHMS_SHARED_OBJ_DIR) ]; then mkdir -p $(ALGORITHMS_SHARED_OBJ_DIR); fi
 	@if [ ! -d $(CONFIG_OBJ_DIR) ]; then mkdir -p $(CONFIG_OBJ_DIR); fi
 	@if [ ! -d $(IO_OBJ_DIR) ]; then mkdir -p $(IO_OBJ_DIR); fi
+	@if [ ! -d $(IO_SHARED_OBJ_DIR) ]; then mkdir -p $(IO_SHARED_OBJ_DIR); fi
 	@if [ ! -d $(SUBCOMMAND_OBJ_DIR) ]; then mkdir -p $(SUBCOMMAND_OBJ_DIR); fi
 	@if [ ! -d $(UNITTEST_OBJ_DIR) ]; then mkdir -p $(UNITTEST_OBJ_DIR); fi
+	@if [ ! -d $(UNITTEST_SUPPORT_OBJ_DIR) ]; then mkdir -p $(UNITTEST_SUPPORT_OBJ_DIR); fi
 	@if [ ! -d $(INC_DIR) ]; then mkdir -p $(INC_DIR); fi
 	@if [ -e $(INC_DIR)/vg/vg.pb.h ] ; then \
 		HEADER_VER=$$(cat $(INC_DIR)/vg/vg.pb.h | grep GOOGLE_PROTOBUF_VERSION | sed 's/[^0-9]*\([0-9]*\)[^0-9]*/\1/' | head -n1); \
@@ -869,20 +922,31 @@ $(UNITTEST_OBJ_DIR)/%.d: ;
 
 # for rebuilding just vg
 clean-vg:
-	$(RM) -r $(BIN_DIR)/$(EXE)
-	$(RM) -r $(UNITTEST_OBJ_DIR)/*.o $(UNITTEST_OBJ_DIR)/*.d
-	$(RM) -r $(SUBCOMMAND_OBJ_DIR)/*.o $(SUBCOMMAND_OBJ_DIR)/*.d
-	$(RM) -r $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d
+	$(RM) -f $(BIN_DIR)/$(EXE)
+	$(RM) -f $(UNITTEST_SUPPORT_OBJ_DIR)/*.o $(UNITTEST_SUPPORT_OBJ_DIR)/*.d
+	$(RM) -f $(UNITTEST_OBJ_DIR)/*.o $(UNITTEST_OBJ_DIR)/*.d
+	$(RM) -f $(SUBCOMMAND_OBJ_DIR)/*.o $(SUBCOMMAND_OBJ_DIR)/*.d
+	$(RM) -f $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d
+	$(RM) -f $(SHARED_OBJ_DIR)/*.o $(SHARED_OBJ_DIR)/*.d
+	$(RM) -f $(ALGORITHMS_OBJ_DIR)/*.o $(ALGORITHMS_OBJ_DIR)/*.d
+	$(RM) -f $(ALGORITHMS_SHARED_OBJ_DIR)/*.o $(ALGORITHMS_SHARED_OBJ_DIR)/*.d
+	$(RM) -f $(IO_OBJ_DIR)/*.o $(IO_OBJ_DIR)/*.d
+	$(RM) -f $(IO_SHARED_OBJ_DIR)/*.o $(IO_SHARED_OBJ_DIR)/*.d
 	$(RM) -f $(INC_DIR)/vg_git_version.hpp $(INC_DIR)/vg_system_version.hpp
 
 clean: clean-vcflib
+	$(RM) -r $(UNITTEST_BIN_DIR)
 	$(RM) -r $(BIN_DIR)
 	$(RM) -r $(LIB_DIR)
+	$(RM) -r $(UNITTEST_SUPPORT_OBJ_DIR)
 	$(RM) -r $(UNITTEST_OBJ_DIR)
 	$(RM) -r $(SUBCOMMAND_OBJ_DIR)
+	$(RM) -r $(IO_SHARED_OBJ_DIR)
 	$(RM) -r $(IO_OBJ_DIR)
+	$(RM) -r $(ALGORITHMS_SHARED_OBJ_DIR)
 	$(RM) -r $(ALGORITHMS_OBJ_DIR)
 	$(RM) -r $(CONFIG_OBJ_DIR)
+	$(RM) -r $(SHARED_OBJ_DIR)
 	$(RM) -r $(OBJ_DIR)
 	$(RM) -r $(INC_DIR)
 	$(RM) -r share/