X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2FMakefile;h=d36e7acb4a4c68956f3fed6dbcc16d9c042dc729;hb=44428cd6d2c6f24b7fe59e1333d883a5a1a11e12;hp=1008e91cd10f13fd89ddb1ccaa5dac092ab3a337;hpb=17514ff7dafaf019828c50df8869df6bb9f0e331;p=samtools.git

diff --git a/misc/Makefile b/misc/Makefile
index 1008e91..d36e7ac 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 ace2sam wgsim bamcheck
 INCLUDES=	-I..
 SUBDIRS=	.
 
@@ -27,11 +27,20 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 
 lib:
 
+bamcheck:bamcheck.o
+		$(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
+
+bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
+		$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
+
+ace2sam:ace2sam.o
+		$(CC) $(CFLAGS) -o $@ ace2sam.o -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 -L../zlib -lz
+		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
 
 md5sum-lite:md5sum-lite.o
 		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
@@ -40,15 +49,21 @@ md5sum-lite.o:md5.c md5.h
 		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
 
 maq2sam-short:maq2sam.c
-		$(CC) $(CFLAGS) -I../zlib -o $@ maq2sam.c -L../zlib -lz
+		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
 
 maq2sam-long:maq2sam.c
-		$(CC) $(CFLAGS) -I../zlib -DMAQ_LONGREADS -o $@ maq2sam.c -L../zlib -lz
+		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
 
 md5fa.o:md5.h md5fa.c
 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.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