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Merge pull request #3700 from vgteam/lr-giraffe
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Long Read Giraffe
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adamnovak authored Jul 29, 2022
2 parents 371c103 + 694f472 commit fd97f17
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Showing 21 changed files with 5,083 additions and 1,309 deletions.
90 changes: 77 additions & 13 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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.
Expand All @@ -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=""
Expand Down Expand Up @@ -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.
Expand All @@ -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
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand All @@ -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)
Expand Down Expand Up @@ -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"

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)/
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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); \
Expand Down Expand Up @@ -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/
Expand Down
2 changes: 1 addition & 1 deletion deps/vcflib
Submodule vcflib updated 1 files
+15 −2 src/Variant.cpp
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2 comments on commit fd97f17

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vg CI tests complete for merge to master. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 9371 seconds

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vg CI tests complete for branch surject_assertion_hack. View the full report here.

12 tests passed, 0 tests failed and 0 tests skipped in 6856 seconds

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