X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2FMakefile;h=9434399bdc6a08245a013d19c8a598b9151ce644;hb=248e7fec261fb1e5ac4281fb6064989f52c206c8;hp=8a38f54a3cdf2fd01aab1ac8b0723f49ee228ee6;hpb=f93dae0d03856955f9424e8b2aaf261304ca647e;p=samtools.git

diff --git a/misc/Makefile b/misc/Makefile
index 8a38f54..9434399 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
-INCLUDES=
-LIBS=		-lm -lz
+PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim seqtk bamcheck
+INCLUDES=	-I..
 SUBDIRS=	.
 
 .SUFFIXES:.c .o
@@ -21,21 +20,33 @@ 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:
 
-faidx:../faidx.c ../faidx.h
-		$(CC) $(CFLAGS) -DFAIDX_MAIN -o $@ ../faidx.c
+bamcheck:bamcheck.o
+		$(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam
+
+ace2sam:ace2sam.o
+		$(CC) $(CFLAGS) -o $@ ace2sam.o -lz
+
+seqtk:seqtk.o
+		$(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz
+
+wgsim:wgsim.o
+		$(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
 
 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
@@ -46,7 +57,16 @@ maq2sam-long:maq2sam.c
 md5fa.o:md5.h md5fa.c
 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.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
+
+ace2sam.o:ace2sam.c ../kstring.h ../kseq.h
+		$(CC) $(CFLAGS) -c -I.. -o $@ ace2sam.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