File: makefile.linux

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CC=gcc
INCS=-I"$(JAVA_HOME)/include" -I"$(JAVA_HOME)/include/linux"
CFLAGS+=-O3 -Wall -std=c99 -fPIC
LDFLAGS+=-O3 -Wall -std=c99 -fPIC -shared
OBJ=BandedAlignerJNI.o MultiStateAligner11tsJNI.o BBMergeOverlapper.o IceCreamAlignerJNI.o

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

libbbtoolsjni.so: $(OBJ)
	$(CC) -o $@ $^ $(LDFLAGS)

.PHONY: clean

clean:
	rm -f *.o *~ core libbbtoolsjni.so