CC = gcc -O3

all: anchors chaos order mlagan utils/bin2mf utils/bin2bl utils/cextract utils/cstat utils/contigorder utils/countmatch utils/getbounds utils/getlength utils/getranges utils/makeranges utils/rc utils/seqmerge utils/scorealign utils/scorecontigs
clean: 
	rm -f chaos anchors order utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/makeranges utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getranges utils/getlength utils/countmatch utils/*~ utils/scorealign utils/scorecontigs
anchors: anchors.c skiplist.c
	$(CC) -o anchors anchors.c skiplist.c
chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
	$(CC) -o chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
order: order.c diagmatrix.c filebuffer.c
	$(CC) -o order order.c diagmatrix.c filebuffer.c
mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
	$(CC) -o mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
utils/bin2mf: utils/bin2mf.c
	$(CC) -o utils/bin2mf utils/bin2mf.c
utils/bin2bl: utils/bin2bl.c
	$(CC) -o utils/bin2bl utils/bin2bl.c
utils/cextract: utils/cextract.c
	$(CC) -o utils/cextract utils/cextract.c
utils/cstat: utils/cstat.c
	$(CC) -o utils/cstat utils/cstat.c
utils/contigorder: utils/contigorder.c
	$(CC) -o utils/contigorder utils/contigorder.c
utils/countmatch: utils/countmatch.c
	$(CC) -o utils/countmatch utils/countmatch.c
utils/getbounds: utils/getbounds.c
	$(CC) -o utils/getbounds utils/getbounds.c
utils/getlength: utils/getlength.c
	$(CC) -o utils/getlength utils/getlength.c
utils/getranges: utils/getranges.c
	$(CC) -o utils/getranges utils/getranges.c
utils/makeranges: utils/makeranges.c
	$(CC) -o utils/makeranges utils/makeranges.c
utils/rc: utils/rc.c
	$(CC) -o utils/rc utils/rc.c
utils/seqmerge: utils/seqmerge.c
	$(CC) -o utils/seqmerge utils/seqmerge.c
utils/scorealign: utils/scorealign.c
	$(CC) -o utils/scorealign utils/scorealign.c -lm
utils/scorecontigs: utils/scorecontigs.c
	$(CC) -o utils/scorecontigs utils/scorecontigs.c -lm
