r579: after merging Peter's depad changes

[samtools.git] / bcftools / Makefile

diff --git a/bcftools/Makefile b/bcftools/Makefile
index 5a3dc763f8105ba3dc8db43db390a4b13c0ba252..be831de67c2ebdf64586dd79523921fbccda9698 100644 (file)
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -1,9 +1,9 @@
 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 kfunc.o index.o fet.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 $(OMISC)/bedidx.o
 PROG=          bcftools
 INCLUDES=      
 SUBDIRS=       .
@@ -28,14 +28,18 @@ all:$(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