# Makefile for collocation, controlling for local sequence biases using expected k-mer counts

#CFLAGS= -O3 -static -I/r100/burge/shared/include -L/r100/burge/shared/lib -lm -lRmath
CFLAGS= -O3 -I/r100/burge/shared/include 
LDFLAGS = -L/r100/burge/shared/lib -lm -lRmath 

CC=gcc

all: coCOA

coCOA: coCOA.c LSM.o Markov.o SeqIO.o ExpBin.o Timer.o CollStats.o
	$(CC) $(CFLAGS) LSM.o Markov.o SeqIO.o ExpBin.o Timer.o CollStats.o coCOA.c $(LDFLAGS) -o coCOA

LSM.o: LSM.c LSM.h
	$(CC) $(CFLAGS) -c LSM.c

Markov.o: LSM.h SeqIO.h Markov.c Markov.h
	$(CC) $(CFLAGS) -c Markov.c

SeqIO.o: LSM.h SeqIO.c SeqIO.h
	$(CC) $(CFLAGS) -c SeqIO.c

ExpBin.o: ExpBin.c ExpBin.h
	$(CC) $(CFLAGS) -c ExpBin.c

Timer.o: Timer.c Timer.h
	$(CC) $(CFLAGS) -c Timer.c

CollStats.o: CollStats.c CollStats.h
	$(CC) $(CFLAGS) -c CollStats.c

clean:
	-rm *.o
