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Makefile
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Makefile
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all: kmc kmc_dump kmc_tools py_kmc_api
dummy := $(shell git submodule update --init --recursive)
UNAME_S := $(shell uname -s)
UNAME_M := $(shell uname -m)
UNAME_P := $(shell uname -p)
KMC_MAIN_DIR = kmc_core
KMC_CLI_DIR = kmc_CLI
KMC_API_DIR = kmc_api
KMC_DUMP_DIR = kmc_dump
KMC_TOOLS_DIR = kmc_tools
PY_KMC_API_DIR = py_kmc_api
OUT_BIN_DIR = bin
OUT_INCLUDE_DIR = include
D_OS =
D_ARCH =
ifeq ($(UNAME_S),Darwin)
D_OS=MACOS
ifeq ($(UNAME_M),arm64)
D_ARCH=ARM64
else
D_ARCH=X64
endif
else
D_OS=LINUX
D_ARCH=X64
ifeq ($(UNAME_M),arm64)
D_ARCH=ARM64
endif
ifeq ($(UNAME_M),aarch64)
D_ARCH=ARM64
endif
endif
CPU_FLAGS =
STATIC_CFLAGS =
STATIC_LFLAGS =
PY_FLAGS =
ifeq ($(D_OS),MACOS)
CC = g++-11
ifeq ($(D_ARCH),ARM64)
CPU_FLAGS = -march=armv8.4-a
else
CPU_FLAGS = -m64
endif
STATIC_CFLAGS = -static-libgcc -static-libstdc++ -pthread
STATIC_LFLAGS = -static-libgcc -static-libstdc++ -pthread
PY_FLAGS = -Wl,-undefined,dynamic_lookup -fPIC
else
CC = g++
ifeq ($(D_ARCH),ARM64)
CPU_FLAGS = -march=armv8-a
STATIC_CFLAGS =
STATIC_LFLAGS = -static-libgcc -static-libstdc++ -pthread
else
CPU_FLAGS = -m64
STATIC_CFLAGS = -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
STATIC_LFLAGS = -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
endif
PY_FLAGS = -fPIC
endif
CFLAGS = -Wall -O3 -fsigned-char $(CPU_FLAGS) $(STATIC_CFLAGS) -std=c++14
CLINK = -lm $(STATIC_LFLAGS) -O3 -std=c++14
PY_KMC_API_CFLAGS = $(PY_FLAGS) -Wall -shared -std=c++14 -O3
KMC_CLI_OBJS = \
$(KMC_CLI_DIR)/kmc.o
KFF_OBJS = \
$(KMC_MAIN_DIR)/kff_writer.o
KMC_CORE_OBJS = \
$(KMC_MAIN_DIR)/mem_disk_file.o \
$(KMC_MAIN_DIR)/rev_byte.o \
$(KMC_MAIN_DIR)/bkb_writer.o \
$(KMC_MAIN_DIR)/cpu_info.o \
$(KMC_MAIN_DIR)/bkb_reader.o \
$(KMC_MAIN_DIR)/fastq_reader.o \
$(KMC_MAIN_DIR)/timer.o \
$(KMC_MAIN_DIR)/develop.o \
$(KMC_MAIN_DIR)/kb_completer.o \
$(KMC_MAIN_DIR)/kb_storer.o \
$(KMC_MAIN_DIR)/kmer.o \
$(KMC_MAIN_DIR)/splitter.o \
$(KMC_MAIN_DIR)/kb_collector.o \
$(KMC_MAIN_DIR)/kmc_runner.o
ifeq ($(UNAME_S),Darwin)
ifeq ($(D_ARCH),ARM64)
RADULS_OBJS = \
$(KMC_MAIN_DIR)/raduls_neon.o
else
RADULS_OBJS =
endif
else
ifeq ($(D_ARCH),ARM64)
RADULS_OBJS = \
$(KMC_MAIN_DIR)/raduls_neon.o
else
RADULS_OBJS = \
$(KMC_MAIN_DIR)/raduls_sse2.o \
$(KMC_MAIN_DIR)/raduls_sse41.o \
$(KMC_MAIN_DIR)/raduls_avx2.o \
$(KMC_MAIN_DIR)/raduls_avx.o
endif
endif
LIB_ZLIB=3rd_party/cloudflare/libz.a
LIB_KMC_CORE = $(OUT_BIN_DIR)/libkmc_core.a
KMC_DUMP_OBJS = \
$(KMC_DUMP_DIR)/nc_utils.o \
$(KMC_DUMP_DIR)/kmc_dump.o
KMC_API_OBJS = \
$(KMC_API_DIR)/mmer.o \
$(KMC_API_DIR)/kmc_file.o \
$(KMC_API_DIR)/kmer_api.o
KMC_API_SRC_FILES = $(wildcard $(KMC_API_DIR)/*.cpp)
PY_KMC_API_OBJS = $(patsubst $(KMC_API_DIR)/%.cpp,$(PY_KMC_API_DIR)/%.o,$(KMC_API_SRC_FILES))
KMC_TOOLS_OBJS = \
$(KMC_TOOLS_DIR)/kmer_file_header.o \
$(KMC_TOOLS_DIR)/kmc_tools.o \
$(KMC_TOOLS_DIR)/nc_utils.o \
$(KMC_TOOLS_DIR)/parameters_parser.o \
$(KMC_TOOLS_DIR)/parser.o \
$(KMC_TOOLS_DIR)/tokenizer.o \
$(KMC_TOOLS_DIR)/fastq_filter.o \
$(KMC_TOOLS_DIR)/fastq_reader.o \
$(KMC_TOOLS_DIR)/fastq_writer.o \
$(KMC_TOOLS_DIR)/percent_progress.o \
$(KMC_TOOLS_DIR)/kff_info_reader.o
$(LIB_ZLIB):
cd 3rd_party/cloudflare; ./configure; make libz.a
$(KMC_CLI_OBJS) $(KMC_CORE_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(KMC_TOOLS_OBJS): %.o: %.cpp
$(CC) $(CFLAGS) -I 3rd_party/cloudflare -c $< -o $@
$(KMC_MAIN_DIR)/raduls_sse2.o: $(KMC_MAIN_DIR)/raduls_sse2.cpp
$(CC) $(CFLAGS) -msse2 -c $< -o $@
$(KMC_MAIN_DIR)/raduls_sse41.o: $(KMC_MAIN_DIR)/raduls_sse41.cpp
$(CC) $(CFLAGS) -msse4.1 -c $< -o $@
$(KMC_MAIN_DIR)/raduls_avx.o: $(KMC_MAIN_DIR)/raduls_avx.cpp
$(CC) $(CFLAGS) -mavx -c $< -o $@
$(KMC_MAIN_DIR)/raduls_avx2.o: $(KMC_MAIN_DIR)/raduls_avx2.cpp
$(CC) $(CFLAGS) -mavx2 -c $< -o $@
$(KMC_MAIN_DIR)/raduls_neon.o: $(KMC_MAIN_DIR)/raduls_neon.cpp
$(CC) $(CFLAGS) -c $< -o $@
$(LIB_KMC_CORE): $(KMC_CORE_OBJS) $(RADULS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS)
-mkdir -p $(OUT_INCLUDE_DIR)
cp $(KMC_MAIN_DIR)/kmc_runner.h $(OUT_INCLUDE_DIR)/kmc_runner.h
-mkdir -p $(OUT_BIN_DIR)
ar rcs $@ $^
kmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE) $(LIB_ZLIB)
-mkdir -p $(OUT_BIN_DIR)
$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^
kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
-mkdir -p $(OUT_BIN_DIR)
$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^
kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(LIB_ZLIB)
-mkdir -p $(OUT_BIN_DIR)
$(CC) $(CLINK) -I 3rd_party/cloudflare -o $(OUT_BIN_DIR)/$@ $^
$(PY_KMC_API_DIR)/%.o: $(KMC_API_DIR)/%.cpp
$(CC) -c -fPIC -Wall -O3 $(CPU_FLAGS) -std=c++14 $^ -o $@
py_kmc_api: $(PY_KMC_API_OBJS) $(PY_KMC_API_OBJS)
-mkdir -p $(OUT_BIN_DIR)
$(CC) $(PY_KMC_API_CFLAGS) $(PY_KMC_API_DIR)/py_kmc_api.cpp $(PY_KMC_API_OBJS) \
-I $(KMC_API_DIR) \
-I $(PY_KMC_API_DIR)/libs/pybind11/include \
-I `python3 -c "import sysconfig;print(sysconfig.get_paths()['include'])"` \
-o $(OUT_BIN_DIR)/$@`python3-config --extension-suffix`
clean:
-rm -f $(KMC_MAIN_DIR)/*.o
-rm -f $(KMC_API_DIR)/*.o
-rm -f $(KMC_DUMP_DIR)/*.o
-rm -f $(KMC_TOOLS_DIR)/*.o
-rm -f $(PY_KMC_API_DIR)/*.o
-rm -f $(PY_KMC_API_DIR)/*.so
-rm -rf $(OUT_BIN_DIR)
-rm -rf $(OUT_INCLUDE_DIR)
cd 3rd_party/cloudflare; make clean;