Merge remote branch 'remotes/pierre/master' into develop

[samtools.git] / bcftools / Makefile

diff --git a/bcftools/Makefile b/bcftools/Makefile
index ec3fa746a61dcd5cf959898df9b9ec00c59712a1..be831de67c2ebdf64586dd79523921fbccda9698 100644 (file)
--- 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