#C_OPT=-O3 -funroll-loops -march=pentiumpro#C_OPT=-O3 -march=pentiumpro#C_DEBUG=-W -Wall -g#C_DEF=-DUSE_OBSTACKCFLAGS= -OBZ_SRCS=bz_main.c bz_align.c bz_extend.c bz_chain.c bz_dna.c bz_print.c \	bz_table.c bz_census.c bz_hit19.c bz_inner.c util.c seq.c args.c \	edit.c dna.c charvec.c nib.cSR_SRCS=strip_rpts.c util.c seq.c charvec.c nib.cRC_SRCS=revcomp.c util.c seq.c charvec.c nib.cRR_SRCS=restore_rpts.c util.c seq.c charvec.c nib.c dna.cRT_SRCS=repeats_tag.c util.cblastz: $(BZ_SRCS)	$(CC) $(CFLAGS) $(BZ_SRCS) \		$(M) \		-lm \		-o $@strip_rpts : $(SR_SRCS)	$(CC) $(CFLAGS) $(SR_SRCS) -o $@revcomp : $(RC_SRCS)	$(CC) $(CFLAGS) $(RC_SRCS) -o $@restore_rpts : $(RR_SRCS)	$(CC) $(CFLAGS) $(RR_SRCS) -o $@repeats_tag : $(RT_SRCS)	$(CC) $(CFLAGS) $(RT_SRCS) -o $@# This test determines the additional regions aligned, for one very small# dataset, using an approach to human-mouse alignments pioneered by Arian Smit.# We start with human (softmasked) and mouse (softmasked) and the corresponding# RepeatMasker ".out" files, human.out and mouse.out. Lineage-specific are# removed, the sequences are aligned, and the blastz output files are adjusted# as if run on the original sequences.test : blastz strip_rpts revcomp restore_rpts repeats_tag	primate.pl human.out	./repeats_tag human.out.primspec > hum.new.rpts	rodent.pl mouse.out	./repeats_tag mouse.out.rodspec > mus.new.rpts	./strip_rpts human hum.new.rpts > hum.stripped	./strip_rpts mouse mus.new.rpts > mus.stripped	./blastz hum.stripped mus.stripped B=0 | \		./restore_rpts - \		human "\"human\" 1 10001" \		mouse "\"mouse\" 1 10000" \		hum.new.rpts mus.new.rpts \		> restored.blastz	./revcomp mus.stripped > mus.stripped.rev	./blastz hum.stripped mus.stripped.rev B=0 | \		./restore_rpts - \		human "\"human\" 1 10001" \		mouse "\"mouse-\" 1 10000" \		hum.new.rpts mus.new.rpts \		reverse >> restored.blastz	./blastz human mouse > regular.blastz	wc regular.blastz restored.blastzREADME : README.tex	latex README.tex	dvips -Ppdf -G0 -o README.ps README.dvi	ps2pdf README.ps README.pdftarfile : README	mkdir blastz-source	cp README.pdf Makefile *.c *.h human human.out mouse mouse.out \		primate.pl rodent.pl blastz-source	tar -cf - blastz-source | gzip > blastz.tar.gz	rm -rf blastz-sourcedist : tarfile	cp blastz.tar.gz /home/nog/httpd/html/dist