X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=bcftools%2FMakefile;h=be831de67c2ebdf64586dd79523921fbccda9698;hb=9f118264ea012adc21a46d7c03eaad4f9ce7d4d4;hp=b6ab9726a6efa25e1554f7cb28aab4d1fc4a9600;hpb=032937695157a15fb0ce042deda22afc30be1616;p=samtools.git

diff --git a/bcftools/Makefile b/bcftools/Makefile
index b6ab972..be831de 100644
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -1,9 +1,9 @@
 CC=			gcc
-CFLAGS=		-g -Wall #-O2 #-m64 #-arch ppc
+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
+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=		call1.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 $(OMISC)/bedidx.o
 PROG=		bcftools
 INCLUDES=	
 SUBDIRS=	.
@@ -28,10 +28,10 @@ all:$(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 -lpthread
 
 bcf.o:bcf.h
 vcf.o:bcf.h