X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2FMakefile;h=be831de67c2ebdf64586dd79523921fbccda9698;hb=d46afb500a437323dda82920f9fb18324b2dbec0;hp=ec3fa746a61dcd5cf959898df9b9ec00c59712a1;hpb=fd187467e3c5f026a4d934c5b0cb68a42939f6e1;p=samtools.git

diff --git a/bcftools/Makefile b/bcftools/Makefile
index ec3fa74..be831de 100644
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -1,17 +1,17 @@
 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=	-I..
+INCLUDES=	
 SUBDIRS=	.
 
 .SUFFIXES:.c .o
 
 .c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
 
 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 		@target=`echo $@ | sed s/-recur//`; \
@@ -28,14 +28,18 @@ all:$(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 -lpthread
 
 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