CC = gcc 
LIB = 
INCLUDES =

### This will compile the seriell version: 
CFLAGS = -Wall -O2
### Use this line to compile the methylome version:
#CFLAGS = -Wall -O2 -fpic
### Use this line to compile the paralized version:
#CFLAGS = -pthread -DTHREADS -D_REENTRANT -Wall -O2 

OBJ = src/genomemapper/alignseriell.o src/genomemapper/alignthread.o src/genomemapper/alloc.o src/genomemapper/genomemapper.o src/genomemapper/hitseriell.o src/genomemapper/hitthread.o src/genomemapper/hit.o src/genomemapper/index.o src/genomemapper/init.o src/genomemapper/load.o src/genomemapper/print.o src/genomemapper/read.o src/genomemapper/usage.o src/gmindex/alloc.o src/gmindex/index.o src/gmindex/init.o src/gmindex/load.o src/gmindex/gmindex.o src/gmindex/usage.o src/gmindex/write.o

genomemapper: $(OBJ)
	$(CC) $(LIB) $(INCLUDES) $(CFLAGS) -o genomemapper src/genomemapper/alloc.c src/genomemapper/genomemapper.c src/genomemapper/hitseriell.c src/genomemapper/hitthread.c src/genomemapper/hit.c src/genomemapper/index.c src/genomemapper/init.c src/genomemapper/print.c src/genomemapper/read.c src/genomemapper/usage.c src/genomemapper/load.c src/genomemapper/alignseriell.c src/genomemapper/alignthread.c
	$(CC) $(CFLAGS) -o gmindex src/gmindex/gmindex.c src/gmindex/alloc.c src/gmindex/index.c src/gmindex/init.c src/gmindex/load.c src/gmindex/usage.c src/gmindex/write.c

clean:
	rm -f src/genomemapper/*.o src/gmindex/*.o genomemapper gmindex

src/genomemapper/%.o: src/genomemapper/%.c
	$(CC) $(LIB) $(INCLUDES) $(CFLAGS) -c $? -o $@

src/gmindex/%.o: src/gmindex/%.c
	$(CC) $(CFLAGS) -c $? -o $@


