Imported Upstream version 0.1.9

[samtools.git] / bcftools / Makefile

diff --git a/bcftools/Makefile b/bcftools/Makefile
new file mode 100644 (file)
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