X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=misc%2FMakefile;h=d2f8bd8ea56c74709f4f0d426787db3cd6c52dd9;hp=2d7139d4e8a5c62068afb381f47493f8408bc681;hb=HEAD;hpb=67801bf17aa6495879da63ce77a2014759fabc16

diff --git a/misc/Makefile b/misc/Makefile
index 2d7139d..d2f8bd8 100644
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -1,10 +1,10 @@
 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
 OBJS=		
-PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk
 INCLUDES=	-I..
 SUBDIRS=	.
 
@@ -27,11 +27,11 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 
 lib:
 
-afs2:afs2.o
-		$(CC) $(CFLAGS) -o $@ afs2.o -lm -lz -L.. -lbam
+seqtk:seqtk.o
+		$(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz
 
 wgsim:wgsim.o
-		$(CC) $(CFLAGS) -o $@ wgsim.o -lm
+		$(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
 
 md5fa:md5.o md5fa.o md5.h ../kseq.h
 		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
@@ -51,8 +51,11 @@ 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
+seqtk.o:seqtk.c ../khash.h ../kseq.h
+		$(CC) $(CFLAGS) -c -I.. -o $@ seqtk.c
+
+wgsim.o:wgsim.c ../kseq.h
+		$(CC) $(CFLAGS) -c -I.. -o $@ wgsim.c
 
 cleanlocal:
 		rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a