* samtools-0.1.8-1 (r615)

[samtools.git] / misc / Makefile

diff --git a/misc/Makefile b/misc/Makefile
index 1008e91cd10f13fd89ddb1ccaa5dac092ab3a337..6c25c782eb4e2ad784563991bd69922e885737cb 100644 (file)
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -1,6 +1,6 @@
 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=          
@@ -27,11 +27,14 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 
 lib:
 
+afs2:afs2.o
+               $(CC) $(CFLAGS) -o $@ afs2.o -lm -lz -L.. -lbam
+
 wgsim:wgsim.o
                $(CC) $(CFLAGS) -o $@ wgsim.o -lm
 
 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 +43,18 @@ 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
 
+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