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CC= gcc
# Use flags when CFLAGS is not already defined in the environment.
CFLAGS?= -g -Wall -O2
# But always append special flags we need.
CFLAGS+= -fPIC #-m64 #-arch ppc
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE
LOBJS= bgzf.o kstring.o knetfile.o index.o bedidx.o
AOBJS= main.o
PROG= tabix bgzip
INCLUDES=
SUBDIRS= .
LIBPATH=
LIBCURSES=
.SUFFIXES:.c .o
.c.o:
$(CC) -c $(CPPFLAGS) $(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:$(PROG)
lib:libtabix.a
libtabix.so.1:$(LOBJS)
$(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
libtabix.1.dylib:$(LOBJS)
libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
libtabix.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
tabix:lib $(AOBJS)
$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
bgzip:bgzip.o bgzf.o knetfile.o
$(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
TabixReader.class:TabixReader.java
javac -cp .:sam.jar TabixReader.java
kstring.o:kstring.h
knetfile.o:knetfile.h
bgzf.o:bgzf.h knetfile.h
index.o:bgzf.h tabix.h khash.h ksort.h kstring.h
main.o:tabix.h kstring.h bgzf.h
bgzip.o:bgzf.h
bedidx.o:kseq.h khash.h
tabix.pdf:tabix.tex
pdflatex tabix.tex
cleanlocal:
rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log tabix.pdf *.class libtabix.*.dylib libtabix.so*
clean:cleanlocal-recur
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