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Makefile
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CC= gcc
CXX= g++
#CFLAGS= -g -Wall -pg #-O2 -m64 -pg
CFLAGS= -g -Wall -O2 -m64 #-pg
CXXFLAGS= $(CFLAGS)
DFLAGS= -DHAVE_PTHREAD #-DOCC_INTERVAL_DEFAULT=0x80 #-D_FILE_OFFSET_BITS=64
#OBJS= utils.o bwt.o bwtio.o jigsawaln.o bwtgap.o is.o \
# bntseq.o bwtmisc.o stdaln.o simple_dp.o \
# bwaseqio.o bwase.o kstring.o cs2nt.o \
# bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o \
# bwtsw2_chain.o bamlite.o #bwt_lite.o
OBJS= utils.o bwt.o bwtio.o jigsawaln.o bwtgap.o is.o \
bntseq.o bwtmisc.o stdaln.o simple_dp.o \
bwaseqio.o bwase.o kstring.o cs2nt.o \
bamlite.o bwt_lite.o splicesitemap.o splicescore.o
PROG= olego olegoindex #bwtsw #jigsawse
INCLUDES= -I./cz
LIBS= -lm -lz -lpthread -Lbwt_gen -lbwtgen
LIBS2= ./cz/czlib.a
SUBDIRS= . bwt_gen cz
.SUFFIXES:.c .o .cc
.c.o:
$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
.cpp.o:
$(CXX) -c $(CXXFLAGS) $(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)" \
INCLUDES="$(INCLUDES)" $$target || exit 1; \
cd $$wdir; \
done;
lib:
olegoindex:lib-recur $(OBJS) jigsawindex.o
$(CXX) $(CFLAGS) $(DFLAGS) $(OBJS) jigsawindex.o -o $@ $(LIBS) $(LIBS2)
olego:lib-recur $(OBJS) jigsaw.o
$(CXX) $(CFLAGS) $(DFLAGS) $(OBJS) jigsaw.o -o $@ $(LIBS) $(LIBS2)
bwtsw:lib-recur $(OBJS) bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwtsw2_chain.o
$(CXX) $(CFLAGS) $(DFLAGS) $(OBJS) bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwtsw2_chain.o -o $@ $(LIBS) $(LIBS2)
jigsawse:lib-recur $(OBJS) jigsawse.o
$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) jigsawse.o -o $@ $(LIBS)
bwt.o:bwt.h
bwtio.o:bwt.h
jigsaw.o:bwt.h jigsawaln.h kseq.h bwase.h splicesitemap.h splicescore.h
bwt1away.o:bwt.h jigsawaln.h
bwt2fmv.o:bwt.h
bntseq.o:bntseq.h
bwtgap.o:bwtgap.h jigsawaln.h bwt.h
bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_main.o:bwtsw2.h
splicescore.o:bntseq.h bwaseqio.h splicescore.h
cleanlocal:
rm -f gmon.out *.o a.out $(PROG) *~ *.a
clean:cleanlocal-recur