X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2FMakefile;fp=bcftools%2FMakefile;h=8b890ba67e7ca5146bfc05e533884f52bc8d371a;hp=0000000000000000000000000000000000000000;hb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522;hpb=cb12a866906ec4ac644de0e658679261c82ab098

diff --git a/bcftools/Makefile b/bcftools/Makefile
new file mode 100644
index 0000000..8b890ba
--- /dev/null
+++ b/bcftools/Makefile
@@ -0,0 +1,51 @@
+CC=			gcc
+CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+LOBJS=		bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
+OMISC=		..
+AOBJS=		call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
+PROG=		bcftools
+INCLUDES=	
+SUBDIRS=	.
+
+.SUFFIXES:.c .o
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+			cd $$wdir; \
+		done;
+
+all:$(PROG)
+
+lib:libbcf.a
+
+libbcf.a:$(LOBJS)
+		$(AR) -cru $@ $(LOBJS)
+
+bcftools:lib $(AOBJS)
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -lbcf
+
+bcf.o:bcf.h
+vcf.o:bcf.h
+index.o:bcf.h
+bcfutils.o:bcf.h
+prob1.o:prob1.h bcf.h
+call1.o:prob1.h bcf.h
+bcf2qcall.o:bcf.h
+main.o:bcf.h
+
+bcf.pdf:bcf.tex
+		pdflatex bcf
+
+cleanlocal:
+		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
+
+clean:cleanlocal-recur