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CC=gcc
CFLAGS=-Wall -std=c++11 -g -fPIC -O3 $(FLAGS)
LIBHDF5=$(shell pkg-config --libs-only-L hdf5-serial | sed 's/^-L//')
HDF5_LIB=$(shell pkg-config --libs hdf5-serial)
HDF5_INCLUDE=$(shell pkg-config --cflags hdf5-serial)
LIBBWA=/usr/lib/libbwa.a
BWA_LIB=$(LIBBWA)
BWA_INCLUDE=-I/usr/include/bwa
LIBS=$(HDF5_LIB) $(BWA_LIB) -lstdc++ -lz -ldl -pthread -lm
INCLUDE= -I/usr/include/fast5/ $(shell pybind11-config --includes) $(HDF5_INCLUDE) $(BWA_INCLUDE)
SRC=src
BUILD=build
BIN=bin
LIB=lib
#INCLUDE=include
_COMMON_OBJS=mapper.o seed_tracker.o range.o event_detector.o normalizer.o chunk.o read_buffer.o fast5_reader.o event_profiler.o #sync_out.o
_MAP_ORD_OBJS=$(_COMMON_OBJS) realtime_pool.o map_pool_ord.o uncalled_map_ord.o
_MAP_OBJS=$(_COMMON_OBJS) map_pool.o uncalled_map.o
_SIM_OBJS=$(_COMMON_OBJS) realtime_pool.o client_sim.o uncalled_sim.o
_DTW_OBJS=dtw_test.o fast5_reader.o read_buffer.o normalizer.o chunk.o event_detector.o range.o
_ALL_OBJS=$(_COMMON_OBJS) realtime_pool.o map_pool.o uncalled_map.o uncalled_map_ord.o client_sim.o uncalled_sim.o dtw_test.o
MAP_OBJS = $(patsubst %, $(BUILD)/%, $(_MAP_OBJS))
MAP_ORD_OBJS = $(patsubst %, $(BUILD)/%, $(_MAP_ORD_OBJS))
SIM_OBJS = $(patsubst %, $(BUILD)/%, $(_SIM_OBJS))
DTW_OBJS = $(patsubst %, $(BUILD)/%, $(_DTW_OBJS))
ALL_OBJS = $(patsubst %, $(BUILD)/%, $(_ALL_OBJS))
DEPENDS := $(patsubst %.o, %.d, $(ALL_OBJS))
MAP_BIN = $(BIN)/uncalled_map
MAP_ORD_BIN = $(BIN)/uncalled_map_ord
SIM_BIN = $(BIN)/uncalled_sim
DTW_BIN = $(BIN)/dtw_test
all: dirs $(MAP_BIN) $(MAP_ORD_BIN) $(SIM_BIN) $(DTW_BIN)
#$(BIN)/%.o:src/%.c
# $(CC) -c $< -o $@
$(MAP_BIN): $(MAP_OBJS) $(LIBHDF5) $(LIBBWA)
$(CC) $(CFLAGS) $(MAP_OBJS) -o $@ $(LIBS)
$(MAP_ORD_BIN): $(MAP_ORD_OBJS) $(LIBHDF5) $(LIBBWA)
$(CC) $(CFLAGS) $(MAP_ORD_OBJS) -o $@ $(LIBS)
$(SIM_BIN): $(SIM_OBJS) $(LIBHDF5) $(LIBBWA)
$(CC) $(CFLAGS) $(SIM_OBJS) -o $@ $(LIBS)
$(DTW_BIN): $(DTW_OBJS) $(LIBHDF5) $(LIBBWA)
$(CC) $(CFLAGS) $(DTW_OBJS) -o $@ $(LIBS)
#inspired by https://github.com/jts/nanopolish/blob/master/Makefile
$(LIBHDF5):
cd submods/hdf5 && \
./configure --enable-threadsafe --disable-hl --prefix=`pwd` --enable-shared=no --with-pic=yes || exit 255
make -j 8 -C submods/hdf5 && make -C submods/hdf5 install
#--CFLAGS="-fPIC"
$(LIBBWA):
make -C submods/bwa -f ../../src/Makefile_bwa
-include $(DEPENDS)
$(BUILD)/%.o: $(SRC)/%.cpp $(LIBHDF5) $(LIBBWA)
$(CC) $(CFLAGS) -MMD -MP -c $< -o $@ $(INCLUDE)
DIRS: $(BIN) $(BUILD)
.PHONY: dirs
dirs: $(BIN)/ $(BUILD)/
$(BIN)/:
mkdir -p $@
$(BUILD)/:
mkdir -p $@
clean:
rm -rf $(BUILD)
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