Makefile

# Makefile for the popbam program
CC=               gcc
CFLAGS=           -D_FILE_OFFSET_BITS=64
CXX=              g++
CXXFLAGS=         -D_FILE_OFFSET_BITS=64 -std=c++0x
C_RELEASE_FLAGS=  -Wno-unused -Wno-sign-compare -Wno-write-strings -O2
C_DEBUG_FLAGS=    -Wall -ggdb -DDEBUG
C_PROFILE_FLAGS=  -Wall -O2 -pg
CSOURCES=          bam_aux.c bam.c bam_index.c faidx.c kstring.c bgzf.c \
                   sam_header.c bam_import.c razf.c sam.c bam_pileup.c
CXXSOURCES=        popbam.cpp pop_utils.cpp pop_sample.cpp pop_tree.cpp \
                   pop_snp.cpp pop_nucdiv.cpp pop_ld.cpp pop_sfs.cpp \
                   pop_diverge.cpp pop_haplo.cpp getopt.cpp gamma.cpp
OBJS=              popbam.o pop_utils.o pop_sample.o pop_tree.o \
                   pop_snp.o pop_nucdiv.o pop_ld.o pop_sfs.o pop_diverge.o \
                   pop_haplo.o getopt_pp.o gamma.o\
                   bam_aux.o bam.o bam_index.o faidx.o kstring.o bgzf.o \
                   sam_header.o bam_import.o razf.o sam.o bam_pileup.o
PROG=              popbam
LIBFLAGS=          -lz -lm
INSTALL_DIR=       /usr/local/bin

all: CXXFLAGS +=  $(C_RELEASE_FLAGS)
all: CFLAGS += $(C_RELEASE_FLAGS)
all: $(PROG)

.PHONY: debug
debug: CXXFLAGS += $(C_DEBUG_FLAGS)
debug: CFLAGS += $(C_DEBUG_FLAGS)
debug: $(PROG)

.PHONY: release
release: CXXFLAGS += $(C_RELEASE_FLAGS)
release: CFLAGS += $(C_RELEASE_FLAGS)
release: $(PROG)

.PHONY: profile
profile: CXXFLAGS += $(C_PROFILE_FLAGS)
profile: CFLAGS += $(C_PROFILE_FLAGS)
profile: $(PROG)

$(PROG): $(OBJS)
	$(CXX) -o $@ $(OBJS) $(LIBFLAGS)

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

%.o : %.cpp
	$(CXX) $(CXXFLAGS) -c -o $@ $<

.PHONY: install
install: $(PROG)
	install -m 755 $(PROG) $(INSTALL_DIR)

.PHONY: clean
clean:
	rm -rf $(PROG) $(OBJS)