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debian/2.2+dfsg-1

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all: kmc
	
KMC_BIN_DIR = bin
KMC_MAIN_DIR = kmer_counter
KMC_API_DIR = kmc_api
KMC_DUMP_DIR = kmc_dump

CC 	= g++
CFLAGS	= -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 
CLINK	= -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 

DISABLE_ASMLIB = false

KMC_OBJS = \
$(KMC_MAIN_DIR)/kmer_counter.o \
$(KMC_MAIN_DIR)/mmer.o \
$(KMC_MAIN_DIR)/mem_disk_file.o \
$(KMC_MAIN_DIR)/rev_byte.o \
$(KMC_MAIN_DIR)/bkb_writer.o \
$(KMC_MAIN_DIR)/bkb_reader.o \
$(KMC_MAIN_DIR)/fastq_reader.o \
$(KMC_MAIN_DIR)/timer.o \
$(KMC_MAIN_DIR)/radix.o \
$(KMC_MAIN_DIR)/kb_completer.o \
$(KMC_MAIN_DIR)/kb_storer.o \
$(KMC_MAIN_DIR)/kmer.o

KMC_LIBS = \
$(KMC_MAIN_DIR)/libs/libz.a \
$(KMC_MAIN_DIR)/libs/libbz2.a

KMC_DUMP_OBJS = \
$(KMC_DUMP_DIR)/nc_utils.o \
$(KMC_API_DIR)/mmer.o \
$(KMC_DUMP_DIR)/kmc_dump.o \
$(KMC_API_DIR)/kmc_file.o \
$(KMC_API_DIR)/kmer_api.o



ifeq ($(DISABLE_ASMLIB),true)
	CFLAGS += -DDISABLE_ASMLIB
else
	KMC_LIBS += \
	$(KMC_MAIN_DIR)/libs/alibelf64.a 
endif 	


.cpp.o:
	$(CC) $(CFLAGS) -c $< -o $@

kmc: $(KMC_OBJS)
	-mkdir -p $(KMC_BIN_DIR)
	$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^ $(KMC_LIBS)
kmc_dump: $(KMC_DUMP_OBJS)
	-mkdir -p $(KMC_BIN_DIR)
	$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
clean:
	-rm $(KMC_MAIN_DIR)/*.o
	-rm $(KMC_API_DIR)/*.o
	-rm $(KMC_DUMP_DIR)/*.o
	-rm -rf bin

all: kmc kmc_dump