preliminary contrast variant caller

[samtools.git] / bcftools / Makefile

diff --git a/bcftools/Makefile b/bcftools/Makefile
index ec3fa746a61dcd5cf959898df9b9ec00c59712a1..e3b92e9d29f96734495a4acb0c536642a1918d42 100644 (file)
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -1,17 +1,17 @@
 CC=                    gcc
-CFLAGS=                -g -Wall -O2 #-fPIC #-m64 #-arch ppc
-DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-LOBJS=         bcf.o bcfutils.o prob1.o index.o
+CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
+DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_BCF_QUAD
+LOBJS=         bcf.o vcf.o bcfutils.o prob1.o kfunc.o index.o fet.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
 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//`; \