X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2FMakefile;h=6c25c782eb4e2ad784563991bd69922e885737cb;hb=8b0f98e2ac96b5ab07fd482cbaaa06d458254a90;hp=de37cd489281b5e6e43b645c825fcd7a471a4fbb;hpb=38c2703b74ff9a045933206123c86c4e8f999d14;p=samtools.git

diff --git a/misc/Makefile b/misc/Makefile
index de37cd4..6c25c78 100644
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -1,12 +1,11 @@
 CC=			gcc
 CXX=		g++
-CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
+CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
 CXXFLAGS=	$(CFLAGS)
-DFLAGS=		#-D_FILE_OFFSET_BITS=64
+DFLAGS=		-D_FILE_OFFSET_BITS=64
 OBJS=		
-PROG=		faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
-INCLUDES=
-LIBS=		-lm -lz
+PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+INCLUDES=	-I..
 SUBDIRS=	.
 
 .SUFFIXES:.c .o
@@ -21,24 +20,27 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 		wdir=`pwd`; \
 		list='$(SUBDIRS)'; for subdir in $$list; do \
 			cd $$subdir; \
-			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
 				INCLUDES="$(INCLUDES)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
 
 lib:
 
+afs2:afs2.o
+		$(CC) $(CFLAGS) -o $@ afs2.o -lm -lz -L.. -lbam
+
 wgsim:wgsim.o
 		$(CC) $(CFLAGS) -o $@ wgsim.o -lm
 
-faidx:../faidx.c ../faidx.h
-		$(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
-
 md5fa:md5.o md5fa.o md5.h ../kseq.h
 		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
 
-md5sum-lite:md5.c md5.h
-		$(CC) $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+md5sum-lite:md5sum-lite.o
+		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
+
+md5sum-lite.o:md5.c md5.h
+		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
 
 maq2sam-short:maq2sam.c
 		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
@@ -49,7 +51,10 @@ maq2sam-long:maq2sam.c
 md5fa.o:md5.h md5fa.c
 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
 
+afs2.o:afs2.c ../bam.h
+		$(CC) $(CFLAGS) -c -I.. -o $@ afs2.c
+
 cleanlocal:
-		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+		rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a
 
 clean:cleanlocal-recur