rename Makefile.std as Makefile. GNU building systerm is not ready and may take some...

[samtools.git] / misc / Makefile

diff --git a/misc/Makefile b/misc/Makefile
new file mode 100644 (file)
index 0000000..0f65881
--- /dev/null
+++ b/misc/Makefile
@@ -0,0 +1,58 @@
+CC=                    gcc
+CXX=           g++
+CFLAGS=                -g -Wall -O2 -m64 #-arch ppc
+CXXFLAGS=      $(CFLAGS)
+DFLAGS=                #-D_FILE_OFFSET_BITS=64
+OBJS=          
+PROG=          faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+INCLUDES=      -I..
+LIBS=          -lm -lz
+SUBDIRS=       .
+
+.SUFFIXES:.c .o
+
+.c.o:
+               $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+lib-recur all-recur clean-recur cleanlocal-recur install-recur:
+               @target=`echo $@ | sed s/-recur//`; \
+               wdir=`pwd`; \
+               list='$(SUBDIRS)'; for subdir in $$list; do \
+                       cd $$subdir; \
+                       $(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+                               INCLUDES="$(INCLUDES)" $$target || exit 1; \
+                       cd $$wdir; \
+               done;
+
+lib:
+
+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: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
+
+maq2sam-long:maq2sam.c
+               $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
+
+md5fa.o:md5.h md5fa.c
+               $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
+
+cleanlocal:
+               rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+
+clean:cleanlocal-recur