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makefile
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CWD:=$(shell pwd)
SRC_DIR:=$(CWD)/src
TEST_SRC_DIR:=$(CWD)/src/test
BIN_DIR:=$(CWD)/bin
OBJ_DIR:=$(CWD)/obj
TEST_OBJ_DIR:=$(CWD)/obj/test
LIB_DIR:= $(CWD)/lib
DEP_DIR:= $(CWD)/deps
CXXFLAGS += -std=c++11 -g
ifeq ($(INCLUDE_FLAGS),)
# Include flags may be set by library user
INCLUDE_FLAGS:= -I$(SRC_DIR) -I$(TEST_SRC_DIR) -I$(DEP_DIR)/htslib
endif
LIBS := -L. -L$(DEP_DIR)/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread
LIBHTS := $(DEP_DIR)/htslib/libhts.a
PROBABILITY_DEPS := $(SRC_DIR)/probability.hpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp $(SRC_DIR)/input_haplotype.hpp $(SRC_DIR)/penalty_set.hpp $(SRC_DIR)/delay_multiplier.hpp $(SRC_DIR)/math.hpp $(SRC_DIR)/DP_map.hpp $(SRC_DIR)/row_set.hpp
CORE_OBJ := $(OBJ_DIR)/math.o $(OBJ_DIR)/reference.o $(OBJ_DIR)/probability.o $(OBJ_DIR)/input_haplotype.o $(OBJ_DIR)/delay_multiplier.o $(OBJ_DIR)/DP_map.o $(OBJ_DIR)/penalty_set.o $(OBJ_DIR)/allele.o $(OBJ_DIR)/row_set.o
TREE_OBJ := $(OBJ_DIR)/haplotype_state_node.o $(OBJ_DIR)/haplotype_state_tree.o $(OBJ_DIR)/haplotype_manager.o $(OBJ_DIR)/set_of_extensions.o $(OBJ_DIR)/reference_sequence.o
all : build_dirs tests interface libs serializer profiler
.PHONY: build_dirs libs clean
build_dirs:
if [ ! -d $(OBJ_DIR) ]; then mkdir -p $(OBJ_DIR); fi
if [ ! -d $(TEST_OBJ_DIR) ]; then mkdir -p $(TEST_OBJ_DIR); fi
if [ ! -d $(BIN_DIR) ]; then mkdir -p $(BIN_DIR); fi
if [ ! -d $(LIB_DIR) ]; then mkdir -p $(LIB_DIR); fi
if [ ! -d $(DEP_DIR) ]; then mkdir -p $(DEP_DIR); fi
libs : build_dirs $(LIB_DIR)/libsublinearLS.a $(CORE_OBJ)
clean:
rm -f $(BIN_DIR)/* $(OBJ_DIR)/*.o $(TEST_OBJ_DIR)/*.o $(LIB_DIR)/*
tests : $(TEST_OBJ_DIR)/test.o $(CORE_OBJ) $(LIBHTS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/tests $(LIBS)
tree_tests : $(TEST_OBJ_DIR)/tree_tests.o $(CORE_OBJ) $(TREE_OBJ) $(LIBHTS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/tree_tests $(LIBS)
speed_tree : $(TEST_OBJ_DIR)/speed_tree.o $(CORE_OBJ) $(TREE_OBJ) $(LIBHTS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/speed_tree $(LIBS)
interface : $(OBJ_DIR)/linhapexample.o $(OBJ_DIR)/interface.o $(CORE_OBJ) $(TREE_OBJ) $(LIBHTS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/linhapexample $(LIBS)
serializer : $(OBJ_DIR)/serialize_index.o $(CORE_OBJ) $(LIBHTS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/serializer $(LIBS)
profiler : $(OBJ_DIR)/profiler.o $(CORE_OBJ)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/profiler $(LIBS)
$(LIB_DIR)/libsublinearLS.a : $(CORE_OBJ) $(TREE_OBJ)
ar rc $@ $^
ranlib $@
$(OBJ_DIR)/allele.o : $(SRC_DIR)/allele.cpp $(SRC_DIR)/allele.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/linhapexample.o : $(SRC_DIR)/linhapexample.c $(SRC_DIR)/interface.h $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -std=c11 $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/interface.o : $(SRC_DIR)/interface.cpp $(SRC_DIR)/interface.h $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/haplotype_state_node.o : $(SRC_DIR)/haplotype_state_node.cpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/haplotype_state_tree.o : $(SRC_DIR)/haplotype_state_tree.cpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/haplotype_manager.o : $(SRC_DIR)/haplotype_manager.cpp $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(TEST_OBJ_DIR)/speed_tree.o : $(TEST_SRC_DIR)/speed_tree.cpp $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/delay_multiplier.o : $(SRC_DIR)/delay_multiplier.cpp $(SRC_DIR)/delay_multiplier.hpp $(SRC_DIR)/math.hpp $(SRC_DIR)/DP_map.hpp $(SRC_DIR)/row_set.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/DP_map.o : $(SRC_DIR)/DP_map.cpp $(SRC_DIR)/math.hpp $(SRC_DIR)/DP_map.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/input_haplotype.o : $(SRC_DIR)/input_haplotype.cpp $(SRC_DIR)/input_haplotype.hpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/math.o : $(SRC_DIR)/math.cpp $(SRC_DIR)/math.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/probability.o : $(SRC_DIR)/probability.cpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/penalty_set.o : $(SRC_DIR)/penalty_set.cpp $(SRC_DIR)/penalty_set.hpp $(SRC_DIR)/math.hpp $(SRC_DIR)/DP_map.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/reference.o : $(SRC_DIR)/reference.cpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp $(SRC_DIR)/row_set.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/reference_sequence.o : $(SRC_DIR)/reference_sequence.cpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/row_set.o : $(SRC_DIR)/row_set.cpp $(SRC_DIR)/row_set.hpp $(SRC_DIR)/allele.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/set_of_extensions.o : $(SRC_DIR)/set_of_extensions.cpp $(SRC_DIR)/set_of_extensions.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(TEST_OBJ_DIR)/test.o : $(TEST_SRC_DIR)/test.cpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(TEST_OBJ_DIR)/tree_tests.o : $(TEST_SRC_DIR)/tree_tests.cpp $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/serialize_index.o : $(SRC_DIR)/serialize_index.cpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp $(SRC_DIR)/row_set.hpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(OBJ_DIR)/profiler.o : $(SRC_DIR)/test/profiler.cpp $(PROBABILITY_DEPS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
$(LIBHTS) :
cd deps/htslib && make