CC = gcc
CFLAGS = -Wall -g -std=c99 #-O2
OBJS = main.o read_seq.o background.o genseq.o average_count.o
EXE  = kmerFreq simulateMarkovSeq aveCount
LIBS = -lm

all : kmerFreq simulateMarkovSeq aveCount finish

kmerFreq:	main.o read_seq.o background.o
	$(CC) $(CFLAGS) -o kmerFreq main.o read_seq.o background.o $(LIBS)

simulateMarkovSeq: genseq.o background.o read_seq.o
	$(CC) $(CFLAGS) -o simulateMarkovSeq genseq.o background.o read_seq.o $(LIBS)

aveCount: average_count.o
	$(CC) $(CFLAGS) -o aveCount average_count.o $(LIBS)

genseq.o: genseq.c background.h defines.h
	$(CC) $(CFLAGS) -c genseq.c

main.o:	main.c defines.h background.h
	$(CC) $(CFLAGS) -c main.c

read_seq.o: read_seq.c defines.h background.h
	$(CC) $(CFLAGS) -c read_seq.c

background.o:	background.c background.h defines.h
	$(CC) $(CFLAGS) -c background.c

average_count.o:	average_count.c
	$(CC) $(CFLAGS) -c average_count.c

finish:
	@echo  "All done."
clean:
	rm ${OBJS} ${EXE}

