X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2FMakefile;h=9b6f8633101cab4ccd8697d489c36091cd808892;hb=3384f6c6c1642ada4edae9204ca1202672de7d5a;hp=7fdf41f6b26583bca9641c36ecaadfef468703fe;hpb=6f1c7227019c299bd9df4c4187ca29e0baad1c4b;p=samtools.git

diff --git a/bcftools/Makefile b/bcftools/Makefile
index 7fdf41f..9b6f863 100644
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -1,9 +1,9 @@
 CC=			gcc
-CFLAGS=		-g -Wall -O2 #-fPIC #-m64 #-arch ppc
+CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
 DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-LOBJS=		bcf.o bcfutils.o prob1.o index.o
+LOBJS=		bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
 OMISC=		..
-AOBJS=		vcfout.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
+AOBJS=		call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
 PROG=		bcftools
 INCLUDES=	
 SUBDIRS=	.
@@ -28,14 +28,18 @@ all:$(PROG)
 lib:libbcf.a
 
 libbcf.a:$(LOBJS)
-		$(AR) -cru $@ $(LOBJS)
+		$(AR) -csru $@ $(LOBJS)
 
 bcftools:lib $(AOBJS)
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -lbcf
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz
 
 bcf.o:bcf.h
+vcf.o:bcf.h
+index.o:bcf.h
+bcfutils.o:bcf.h
 prob1.o:prob1.h bcf.h
-vcfout.o:bcf.h prob1.h
+call1.o:prob1.h bcf.h
+bcf2qcall.o:bcf.h
 main.o:bcf.h
 
 bcf.pdf:bcf.tex