| 1 |
GCLDIR := ../gclib |
| 2 |
#if you just built samtools (using `make`) in a local directory |
| 3 |
#you can point both BAM_INCDIR and BAM_LIBDIR to that directory |
| 4 |
#(libbam.a file should be there) |
| 5 |
BAM_INCDIR := /opt/geo/include/bam |
| 6 |
BAM_LIBDIR := /opt/geo/lib |
| 7 |
|
| 8 |
SEARCHDIRS := -I. -I${GCLDIR} -I${BAM_INCDIR} |
| 9 |
|
| 10 |
SYSTYPE := $(shell uname) |
| 11 |
|
| 12 |
MACHTYPE := $(shell uname -m) |
| 13 |
ifeq ($(MACHTYPE), i686) |
| 14 |
MARCH = -march=i686 |
| 15 |
else |
| 16 |
MARCH = |
| 17 |
endif |
| 18 |
|
| 19 |
CC := g++ |
| 20 |
|
| 21 |
BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) \ |
| 22 |
-D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti |
| 23 |
|
| 24 |
#add the link-time optimization flag if gcc version > 4.5 |
| 25 |
GCC_VERSION:=$(subst ., ,$(shell gcc -dumpversion)) |
| 26 |
GCC_MAJOR:=$(word 1,$(GCC_VERSION)) |
| 27 |
GCC_MINOR:=$(word 2,$(GCC_VERSION)) |
| 28 |
#GCC_SUB:=$(word 3,$(GCC_VERSION)) |
| 29 |
GCC_SUB:=x |
| 30 |
|
| 31 |
GCC45OPTS := |
| 32 |
GCC45OPTMAIN := |
| 33 |
|
| 34 |
ifeq ($(findstring debug,$(MAKECMDGOALS)),) |
| 35 |
CFLAGS := -O2 -DNDEBUG $(BASEFLAGS) |
| 36 |
LDFLAGS := -L${BAM_LIBDIR} |
| 37 |
ifeq ($(shell expr $(GCC_MAJOR).$(GCC_MINOR) '>=' 4.5),1) |
| 38 |
CFLAGS += -flto |
| 39 |
GCC45OPTS := -flto |
| 40 |
GCC45OPTMAIN := -fwhole-program |
| 41 |
endif |
| 42 |
else |
| 43 |
CFLAGS := -g -DDEBUG $(BASEFLAGS) |
| 44 |
LDFLAGS := -g -L${BAM_LIBDIR} |
| 45 |
endif |
| 46 |
|
| 47 |
%.o : %.cpp |
| 48 |
${CC} ${CFLAGS} -c $< -o $@ |
| 49 |
|
| 50 |
# C/C++ linker |
| 51 |
|
| 52 |
LINKER := g++ |
| 53 |
LIBS := -lz -lbam |
| 54 |
OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArgs.o ${GCLDIR}/GStr.o \ |
| 55 |
${GCLDIR}/GBam.o |
| 56 |
# ${GCLDIR}/gdna.o ${GCLDIR}/codons.o ${GCLDIR}/gff.o ${GCLDIR}/GStr.o \ |
| 57 |
# ${GCLDIR}/GFastaIndex.o gff_utils.o |
| 58 |
|
| 59 |
.PHONY : all |
| 60 |
all: bamread |
| 61 |
debug: bamread |
| 62 |
version: ; @echo "GCC Version is: "$(GCC_MAJOR)":"$(GCC_MINOR)":"$(GCC_SUB) |
| 63 |
@echo "> GCC Opt. string is: "$(GCC45OPTS) |
| 64 |
$(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/GBase.h |
| 65 |
bamread.o : $(GCLDIR)/GBam.h |
| 66 |
GBam.o : $(GCLDIR)/GBam.h |
| 67 |
|
| 68 |
bamread: $(OBJS) bamread.o |
| 69 |
${LINKER} ${LDFLAGS} $(GCC45OPTS) $(GCC45OPTMAIN) -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 70 |
|
| 71 |
# target for removing all object files |
| 72 |
|
| 73 |
.PHONY : clean |
| 74 |
clean:: |
| 75 |
@${RM} bamread bamread.o* bamread.exe $(OBJS) |
| 76 |
@${RM} core.* |
