CC = gcc
CFLAGS = -D_FILE_OFFSET_BITS=64 -O -g -Wall -Winline -std=c99 -fms-extensions -pthread
CFFLAGS = -D_FILE_OFFSET_BITS=64 -O3 -g -Wall -Winline -std=c99 -fms-extensions -pthread

##

SYSTEM?=$(shell uname -s)

MALLOC_COUNT=
MALLOC_COUNT0=

MALLOC_COUNT_FLAG=0

ifeq ($(SYSTEM),Darwin)
	LFLAGS=-lm -Wno-format
else
	MALLOC_COUNT=malloc_count/malloc_count.c 
	MALLOC_COUNT0=malloc_count/malloc_count0.c 
	LFLAGS= -lm -ldl 
	MALLOC_COUNT_FLAG=1
endif

## -ldl is required by malloc_count 
#LFLAGS = -lm -ldl 

##

HEADERS = *.h

CFILES = gap.c util.c io.c mergegap.c mergehm.c alphabet.c ${MALLOC_COUNT} threads.c multiround.c
CFILES0 = gap.c util.c io.c mergegap.c mergehm.c alphabet.c ${MALLOC_COUNT0} threads.c multiround.c


EXECS = gap1 gap2 gap4 unbwt

# targets not producing a file declared phony
.PHONY: all tools clean tarfile

all: $(EXECS) tools

# BWTs/LCPs merging (assertions enabled and no malloc_count: had some conflicts with -O)
gap:  $(CFILES0) $(HEADERS)
	$(CC) $(CFLAGS) $(CFILES0) -lm -DBSIZE=2 -DMALLOC_COUNT_FLAG=${MALLOC_COUNT_FLAG} -ogap

# fast nodebug versions of the gap algorithm 
gap1:  $(CFILES) $(HEADERS)
	$(CC) $(CFFLAGS) $(CFILES) $(LFLAGS) -DNDEBUG -DBSIZE=1 -DMALLOC_COUNT_FLAG=${MALLOC_COUNT_FLAG} -ogap1

gap2:  $(CFILES) $(HEADERS)
	$(CC) $(CFFLAGS) $(CFILES) $(LFLAGS) -DNDEBUG -DBSIZE=2 -DMALLOC_COUNT_FLAG=${MALLOC_COUNT_FLAG} -ogap2

gap4:  $(CFILES) $(HEADERS)
	$(CC) $(CFFLAGS) $(CFILES) $(LFLAGS) -DNDEBUG -DBSIZE=4 -DMALLOC_COUNT_FLAG=${MALLOC_COUNT_FLAG} -ogap4


##

# executables in tools directory for phases 1 and 3
tools:
	make -C tools

tarfile:
	tar -zcf egap.tgz readme.txt eGap Makefile *.[ch] malloc_count/*.[ch]\
           tools/*.[ch] tools/Makefile tools/*/*.[ch]

clean:
	\rm -f $(EXECS)
	make clean -C tools

remove:
	\rm -f dataset/*.bwt dataset/*.lcp dataset/*.sa_bl dataset/*.sl_bl dataset/*.sa_lcp dataset/*.sa dataset/*.da_bl dataset/*.da dataset/*.size dataset/*.log