Makefile

GCC_CHECK := $(shell gcc --version | head -n 1 | grep -i "clang")

# Check if the OS is macOS or linux
UNAME_S := $(shell uname -s)

ifeq ($(GCC_CHECK),) # gcc
	CXXFLAGS = -std=c++11
else # clang
	CXXFLAGS = -std=c++11 -stdlib=libc++
endif

# add -fno-tree-vectorize to avoid certain vectorization errors in O3 optimization
# right now, we are using -O3 for the best performance, and no vectorization errors were found
EXTRA_FLAGS = -Wall -Wno-misleading-indentation -Wno-unused-function #-Wno-unused-variable -Wno-alloc-size-larger-than

# Define the version number
VERSION=0.0.10
# Get the Git commit hash
GIT_COMMIT := $(shell git rev-parse --short HEAD 2> /dev/null)
ifneq ($(GIT_COMMIT),)
	LONGCALLD_VERSION = $(VERSION)-$(GIT_COMMIT)
else
	LONGCALLD_VERSION = $(VERSION)
endif

HTSLIB_DIR  = ./htslib
HTSLIB      = $(HTSLIB_DIR)/libhts.a

EDLIB_DIR     = ./edlib
EDLIB_INC_DIR = ./edlib/include
EDLIB         = $(EDLIB_DIR)/src/edlib.o

ABPOA_DIR   = ./abPOA
ABPOA_LIB   = ./abPOA/lib/libabpoa.a
ABPOA_INC_DIR = $(ABPOA_DIR)/include

WFA2_DIR    = ./WFA2-lib
WFA2_LIB    = $(WFA2_DIR)/lib/libwfa.a

LIB_PATH    =
LIB         = $(HTSLIB) $(ABPOA_LIB) $(WFA2_LIB) $(LIB_PATH) -lm -lz -lpthread -llzma -lbz2 -lcurl
INCLUDE     = -I $(HTSLIB_DIR) -I $(EDLIB_INC_DIR) -I $(ABPOA_INC_DIR) -I $(WFA2_DIR)

# Try linking against libdeflate
ifeq ($(shell echo "int main() {return 0;}" | ${CC} -x c - $(LIB_PATH) -ldeflate >/dev/null 2>&1 && echo "yes"),yes)
	LIB += -ldeflate
endif

ifeq ($(UNAME_S),Linux) # Linux
	LIB += -lcrypto
	ifneq ($(portable),)
		LIB += -static-libgcc -static-libstdc++
		ifneq ($(opt_lib),)
			LIB = $(HTSLIB) $(ABPOA_LIB) $(WFA2_LIB) -static-libgcc -static-libstdc++ -L${opt_lib} -lm -lz -lpthread -llzma -lbz2 -lcurl -lssl -lcrypto -lssh2 -ldeflate -lzstd 
		else
			ifneq ($(OPT_LIB),)
				LIB = $(HTSLIB) $(ABPOA_LIB) $(WFA2_LIB) -static-libgcc -static-libstdc++ -L${OPT_LIB} -lm -lz -lpthread -llzma -lbz2 -lcurl -lssl -lcrypto -lssh2 -ldeflate -lzstd 
			endif
		endif
	endif
endif

# for debug
ifneq ($(debug),)
	EXTRA_FLAGS  += -D __DEBUG__
endif

ABPOA_GDB_LIB = ./abPOA/lib/libabpoa_sse41.a
ABPOA_NOR_LIB = ./abPOA/lib/libabpoa.a
WFA_GDB_LIB   = ./WFA2-lib/lib/libwfa_gdb.a
WFA_NOR_LIB   = ./WFA2-lib/lib/libwfa.a

# for gdb
ifneq ($(gdb),)
	OPT_FLAGS = -O0 -g
	ABPOA_LIB = $(ABPOA_GDB_LIB)
	WFA2_LIB  = $(WFA_GDB_LIB)
else
	OPT_FLAGS = -O3
	ABPOA_LIB = $(ABPOA_NOR_LIB)
	WFA2_LIB  = $(WFA_NOR_LIB)
endif

CFLAGS = $(OPT_FLAGS) $(EXTRA_FLAGS) -DLONGCALLD_VERSION=\"$(LONGCALLD_VERSION)\"

# for gprof
ifneq ($(pg),)
	OPT_FLAGS = -O3
	PG_FLAG   = -pg
	CFLAGS   += -pg
endif

ifneq ($(PREFIX),)
	OUT_PRE_DIR = $(PREFIX)
else
	OUT_PRE_DIR = .
endif

BIN_DIR = $(OUT_PRE_DIR)/bin
INC_DIR = ./include
SRC_DIR = ./src

HTS_ALL = hts_all
EDLIB_ALL = edlib_all
ABPOA_ALL = abpoa_all
WFA2_ALL = wfa2_all
CSOURCE    = $(wildcard ${SRC_DIR}/*.c)
CPPSOURCE  = $(wildcard $(SRC_DIR)/*.cpp)
CPPSOURCE += $(EDLIB_DIR)/src/edlib.cpp

OBJS    = $(CSOURCE:.c=.o) $(CPPSOURCE:.cpp=.o)
BIN     = $(BIN_DIR)/longcallD
ifneq ($(gdb),)
	BIN = $(BIN_DIR)/gdb_longcallD
endif

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

all: $(HTS_ALL) $(EDLIB) $(ABPOA_LIB) $(WFA2_LIB) $(BIN)

$(HTS_ALL): $(HTSLIB)

$(HTSLIB): $(HTSLIB_DIR)/configure.ac
	cd $(HTSLIB_DIR); autoreconf -i; ./configure; make CC=${CC}

$(EDLIB): $(EDLIB_DIR)/src/edlib.cpp $(EDLIB_DIR)/include/edlib.h
	$(CXX) $(CFLAGS) $(CXXFLAGS) -c $< $(INCLUDE) -o $@
$(EDLIB_ALL): $(EDLIB)

$(ABPOA_GDB_LIB): 
	cd $(ABPOA_DIR); make libabpoa gdb=1 sse41=1
$(ABPOA_NOR_LIB):
	cd $(ABPOA_DIR); make libabpoa

$(ABPOA_ALL): $(ABPOA_LIB)

$(WFA2_LIB):
	cd $(WFA2_DIR); make setup lib_wfa CC_FLAGS="$(CC_FLAGS) -O3" 
$(WFA2_ALL): $(WFA2_LIB)


$(BIN): $(OBJS) $(ABPOA_LIB) $(HTSLIB) $(WFA2_LIB)
	if [ ! -d $(BIN_DIR) ]; then mkdir $(BIN_DIR); fi
	$(CXX) $(OBJS) -o $@ $(LIB) $(PG_FLAG)
# 	$(CC) $(OBJS) -o $@ $(LIB) $(PG_FLAG)

$(SRC_DIR)/align.o: $(SRC_DIR)/align.c $(SRC_DIR)/align.h $(SRC_DIR)/utils.h $(SRC_DIR)/bam_utils.h $(SRC_DIR)/seq.h
	$(CC) -c -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES $(CFLAGS) $< $(INCLUDE) -o $@

$(SRC_DIR)/assign_aln_hap.o: $(SRC_DIR)/assign_aln_hap.c $(SRC_DIR)/assign_aln_hap.h $(SRC_DIR)/utils.h $(SRC_DIR)/bam_utils.h
$(SRC_DIR)/bam_utils.o: $(SRC_DIR)/bam_utils.c $(SRC_DIR)/bam_utils.h $(SRC_DIR)/utils.h
$(SRC_DIR)/cgranges.o: $(SRC_DIR)/cgranges.c $(SRC_DIR)/cgranges.h $(SRC_DIR)/khash.h
$(SRC_DIR)/collect_var.o: $(SRC_DIR)/collect_var.c $(SRC_DIR)/collect_var.h $(SRC_DIR)/bam_utils.h
$(SRC_DIR)/kalloc.o: $(SRC_DIR)/kalloc.c $(SRC_DIR)/kalloc.h
$(SRC_DIR)/kmedoids.o : $(SRC_DIR)/kmedoids.c $(SRC_DIR)/kmedoids.h
$(SRC_DIR)/kthread.o: $(SRC_DIR)/kthread.c
$(SRC_DIR)/main.o: $(SRC_DIR)/main.c $(SRC_DIR)/call_var_main.h
$(SRC_DIR)/call_var_main.o: $(SRC_DIR)/bam_utils.c $(SRC_DIR)/call_var_main.c $(SRC_DIR)/call_var_main.h $(SRC_DIR)/main.h $(SRC_DIR)/utils.h $(SRC_DIR)/seq.h \
                            $(SRC_DIR)/collect_var.h
$(SRC_DIR)/seq.o: $(SRC_DIR)/seq.c $(SRC_DIR)/seq.h $(SRC_DIR)/utils.h
$(SRC_DIR)/sdust.o: $(SRC_DIR)/sdust.c $(SRC_DIR)/sdust.h $(SRC_DIR)/kdq.h $(SRC_DIR)/kvec.h
$(SRC_DIR)/utils.o: $(SRC_DIR)/utils.c $(SRC_DIR)/utils.h $(SRC_DIR)/ksort.h $(SRC_DIR)/kseq.h
$(SRC_DIR)/vcf_utils.o: $(SRC_DIR)/vcf_utils.c $(SRC_DIR)/vcf_utils.h $(SRC_DIR)/utils.h

.PHONY: all hts_all abpoa_all wfa2_all clean clean_all clean_hts clean_abpoa clean_wfa2

clean:
	rm -f $(SRC_DIR)/*.o $(BIN)
clean_all:
	rm -f $(SRC_DIR)/*.o $(BIN) $(HTSLIB) $(ABPOA_LIB) $(WFA2_LIB)
clean_hts:
	rm -f $(HTSLIB)
clean_abpoa:
	rm -f $(ABPOA_LIB) $(ABPOA_DIR)/src/*.o
clean_wfa2:
	rm -f $(WFA2_LIB)