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CC= gcc
CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
KNETFILE_O= knetfile.o
LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o \
$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o
AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
bamtk.o kaln.o
PROG= samtools
INCLUDES=
SUBDIRS= . misc
LIBPATH=
LIBCURSES= -lcurses # -lXCurses
.SUFFIXES:.c .o
.c.o:
$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
all-recur lib-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)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
cd $$wdir; \
done;
all:$(PROG)
.PHONY:all lib clean cleanlocal
.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
lib:libbam.a
libbam.a:$(LOBJS)
$(AR) -cru $@ $(LOBJS)
samtools:$(AOBJS) libbam.a
$(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz
razip:razip.o razf.o $(KNETFILE_O)
$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
bgzip:bgzip.o bgzf.o $(KNETFILE_O)
$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz
razip.o:razf.h
bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
sam.o:sam.h bam.h
bam_import.o:bam.h kseq.h khash.h razf.h
bam_pileup.o:bam.h razf.h ksort.h
bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
bam_lpileup.o:bam.h ksort.h
bam_tview.o:bam.h faidx.h bam_maqcns.h
bam_maqcns.o:bam.h ksort.h bam_maqcns.h
bam_sort.o:bam.h ksort.h razf.h
bam_md.o:bam.h faidx.h
glf.o:glf.h
sam_header.o:sam_header.h khash.h
faidx.o:faidx.h razf.h khash.h
faidx_main.o:faidx.h razf.h
libbam.1.dylib-local:$(LOBJS)
libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
libbam.so.1-local:$(LOBJS)
$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
dylib:
@$(MAKE) cleanlocal; \
case `uname` in \
Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
*) echo 'Unknown OS';; \
esac
cleanlocal:
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
clean:cleanlocal-recur
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