| 1 |
– |
# Useful directories |
| 2 |
– |
|
| 3 |
– |
THISCODEDIR := . |
| 1 |
|
GCLDIR := ../gclib |
| 2 |
< |
SEARCHDIRS := -I${THISCODEDIR} -I${GCLDIR} |
| 2 |
> |
SEARCHDIRS := -I. -I${GCLDIR} |
| 3 |
|
|
| 4 |
|
SYSTYPE := $(shell uname) |
| 5 |
|
|
| 10 |
|
MARCH = |
| 11 |
|
endif |
| 12 |
|
|
| 16 |
– |
|
| 13 |
|
CC := g++ |
| 18 |
– |
BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \ |
| 19 |
– |
-D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \ |
| 20 |
– |
-D_REENTRANT |
| 14 |
|
|
| 15 |
+ |
BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \ |
| 16 |
+ |
-D_LARGEFILE_SOURCE -D_REENTRANT -fno-exceptions -fno-rtti |
| 17 |
+ |
|
| 18 |
+ |
#add the link-time optimization flag if gcc version > 4.5 |
| 19 |
+ |
GCC_VERSION:=$(subst ., ,$(shell gcc -dumpversion)) |
| 20 |
+ |
GCC_MAJOR:=$(word 1,$(GCC_VERSION)) |
| 21 |
+ |
GCC_MINOR:=$(word 2,$(GCC_VERSION)) |
| 22 |
+ |
#GCC_SUB:=$(word 3,$(GCC_VERSION)) |
| 23 |
+ |
GCC_SUB:=x |
| 24 |
+ |
|
| 25 |
+ |
GCC45OPTS := |
| 26 |
+ |
GCC45OPTMAIN := |
| 27 |
|
|
| 28 |
|
ifeq ($(findstring debug,$(MAKECMDGOALS)),) |
| 29 |
< |
CFLAGS = -O2 -DNDEBUG $(BASEFLAGS) |
| 30 |
< |
LDFLAGS = |
| 29 |
> |
CFLAGS := -O2 -DNDEBUG $(BASEFLAGS) |
| 30 |
> |
LDFLAGS := |
| 31 |
> |
ifeq ($(shell expr $(GCC_MAJOR).$(GCC_MINOR) '>=' 4.5),1) |
| 32 |
> |
CFLAGS += -flto |
| 33 |
> |
GCC45OPTS := -flto |
| 34 |
> |
GCC45OPTMAIN := -fwhole-program |
| 35 |
> |
endif |
| 36 |
|
else |
| 37 |
< |
CFLAGS = -g -DDEBUG $(BASEFLAGS) |
| 38 |
< |
LDFLAGS = -g |
| 37 |
> |
CFLAGS := -g -DDEBUG $(BASEFLAGS) |
| 38 |
> |
LDFLAGS := -g |
| 39 |
|
endif |
| 40 |
|
|
| 31 |
– |
%.o : %.c |
| 32 |
– |
${CC} ${CFLAGS} -c $< -o $@ |
| 33 |
– |
|
| 34 |
– |
%.o : %.cc |
| 35 |
– |
${CC} ${CFLAGS} -c $< -o $@ |
| 36 |
– |
|
| 37 |
– |
%.o : %.C |
| 38 |
– |
${CC} ${CFLAGS} -c $< -o $@ |
| 39 |
– |
|
| 41 |
|
%.o : %.cpp |
| 42 |
|
${CC} ${CFLAGS} -c $< -o $@ |
| 43 |
|
|
| 43 |
– |
%.o : %.cxx |
| 44 |
– |
${CC} ${CFLAGS} -c $< -o $@ |
| 45 |
– |
|
| 44 |
|
# C/C++ linker |
| 45 |
|
|
| 46 |
< |
LINKER := g++ |
| 47 |
< |
LIBS = |
| 48 |
< |
OBJS = ${GCLDIR}/gff.o ${GCLDIR}/gdna.o ${GCLDIR}/codons.o \ |
| 49 |
< |
${GCLDIR}/GBase.o ${GCLDIR}/GFaSeqGet.o ${GCLDIR}/GStr.o \ |
| 50 |
< |
${GCLDIR}/GArgs.o ${GCLDIR}/gcdb.o ${GCLDIR}/GCdbYank.o ./gffread.o |
| 46 |
> |
LINKER := g++ |
| 47 |
> |
LIBS := |
| 48 |
> |
OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArgs.o ${GCLDIR}/GFaSeqGet.o \ |
| 49 |
> |
${GCLDIR}/gdna.o ${GCLDIR}/codons.o ${GCLDIR}/gff.o ${GCLDIR}/GStr.o \ |
| 50 |
> |
${GCLDIR}/GFastaIndex.o gff_utils.o |
| 51 |
> |
# ${GCLDIR}/gcdb.o ${GCLDIR}/GCdbYank.o |
| 52 |
|
|
| 53 |
|
.PHONY : all |
| 54 |
|
all: gffread |
| 55 |
+ |
|
| 56 |
+ |
version: ; @echo "GCC Version is: "$(GCC_MAJOR)":"$(GCC_MINOR)":"$(GCC_SUB) |
| 57 |
+ |
@echo "> GCC Opt. string is: "$(GCC45OPTS) |
| 58 |
|
debug: gffread |
| 59 |
< |
gffread: ${OBJS} |
| 60 |
< |
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 59 |
> |
$(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/gff.h |
| 60 |
> |
gffread.o : gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h |
| 61 |
> |
gff_utils.o : gff_utils.h $(GCLDIR)/gff.h |
| 62 |
> |
${GCLDIR}/gff.o : ${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh ${GCLDIR}/GHash.hh |
| 63 |
> |
${GCLDIR}/GFaSeqGet.o : ${GCLDIR}/GFaSeqGet.h |
| 64 |
> |
gffread: $(OBJS) gffread.o |
| 65 |
> |
${LINKER} ${LDFLAGS} $(GCC45OPTS) $(GCC45OPTMAIN) -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 66 |
|
|
| 67 |
|
# target for removing all object files |
| 68 |
|
|
| 69 |
|
.PHONY : clean |
| 70 |
|
clean:: |
| 71 |
< |
@${RM} core core.* gffread gffread.exe *.o* ${OBJS} |
| 71 |
> |
@${RM} gffread gffread.o* gffread.exe $(OBJS) |
| 72 |
> |
@${RM} core.* |
| 73 |
|
|
| 74 |
|
|
