slimfastq/Makefile at master · Infinidat/slimfastq · GitHub

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WALL      = -Wall -Werror
FLAGS     = $(WALL) -g -DDO_DEBUG -D_FILE_OFFSET_BITS=64 -std=c++0x
# PROF_DIR  = PROF <=  GCC Bug 47793: relative path turns into absolute
PROF_DIR  =
FLAGS_FAST= -O3 -fomit-frame-pointer -fstrict-aliasing -ffast-math -msse3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
FLAGS_OPT = $(WALL) $(PROF_DIR) $(FLAGS_FAST) -fprofile-use
FLAGS_PROF= $(WALL) $(PROF_DIR) $(FLAGS_FAST) -fprofile-generate
FLAGS_OPT2 = $(WALL) $(PROF_DIR) $(FLAGS_FAST)

# harmless in non-macOS env
export MACOSX_DEPLOYMENT_TARGET=10.14

# ifeq ("$(wildcard ./tmp_samples)","")
ifeq ($(sampdir),)
	TEST_FILES  = $(wildcard samples/*.fq)
	TEST_FILES += $(wildcard samples/*.fastq)
else
	TEST_FILES  = $(wildcard $(sampdir)/*.fq)
	TEST_FILES += $(wildcard $(sampdir)/*.fastq)
endif


all:  slimfastq
opt:  slimfastq.opt

prof-opt.run:
	for l in 1 2 3; do\
		for f in $(TEST_FILES) ; do \
			echo $$f ... ; \
			./slimfastq.prof -f /tmp/mytst -u $$f -O -P -l $$l ; \
			./slimfastq.prof -f /tmp/mytst -u /tmp/mytst.copy -O -d ; \
		done ; \
	done

prof-opt: slimfastq.prof
	make prof-opt.run
	make opt
	make profclean

        # find . -name '*.gcda' -delete
profclean:
	mkdir -p PROF
	find PROF -name '*.gcda' -delete
	mv *.gcda PROF/ || true
	rm *.prof       || true

clean: profclean
	find . -name '*.o' -delete
	rm slimfastq slimfastq.* test-filer || true

gdb: slimfastq.gdb
SOURCES= $(filter-out utest.cpp one.cpp molder.cpp filer.tst.cpp, $(shell ls *.cpp))
HEADERS= $(shell echo *.hpp)
slimfastq.gdb: $(SOURCES) $(HEADERS)
	g++ $(FLAGS) -o $@ $(SOURCES)

valgrind: slimfastq.valgrind
slimfastq.valgrind: $(SOURCES) $(HEADERS)
	g++ $(FLAGS) -DHAPPY_VALGRIND -o $@ $(SOURCES)

.PHONY: slimfastq slimfastq.gdb slimfastq.valgrind test-filer

slimfastq:
	g++ $(FLAGS_OPT2) -o $@ $(SOURCES)
	@ echo "Done."

slimfastq.opt:
	mv PROF/*.gcda . || true
	g++ $(FLAGS_OPT)  -o $@ $(SOURCES)
	mv *.gcda PROF || true
slimfastq.prof:
	g++ $(FLAGS_PROF) -o $@ $(SOURCES)

prof:
	g++ -O3 -fstrict-aliasing -ffast-math -pg -o slimfastq.prof $(SOURCES)

molder: molder.cpp pager.cpp pager.hpp
	g++ $(FLAGS) molder.cpp pager.cpp -o $@

tags:
	etags $(SOURCES) $(HEADERS)

# UTSRC= $(filter-out one.cpp molder.cpp main.cpp, $(shell ls *.cpp))
# UTHDR= $(shell ls *.hpp)
# slimfastq.utest: $(UTSRC) $(UTHDR)
# 	g++ $(FLAGS) $(UTSRC) -o $@
#
# utest: slimfastq.utest
# 	./slimfastq.utest

# small: all
# 	./slimfastq -f ../data/small.fq -u ../data/small.fq -O
# 	./slimfastq -f ../data/small.fq -u ../data/small.fq.tst -O	-d
# 	../data/mydiff.pl ../data/small.fq ../data/small.fq.tst

# time: prof-opt
# 	time ./slimfastq.opt -f ../data/t -u ../data/s.fastq -O
# 	time ./slimfastq.opt -f ../data/t -u ../data/s.fastq.tst -O -d
# 	cmp ../data/s.fastq ../data/s.fastq.tst

test: all
	for l in 1 2 3 4; do \
		for f in $(TEST_FILES) ; do \
			echo $$f $$l...   ; \
			rm /tmp/mytst.* || true; \
			./slimfastq -u $$f -f /tmp/mytst -O -l $$l -q && \
			./slimfastq -u /tmp/mytst.fastq -f /tmp/mytst -O -d && \
			tools/mydiff.pl $$f /tmp/mytst.fastq || break ; \
		done || break ; \
	done

tost: all
	for l in 1 ; do \
		for f in $(TEST_FILES) ; do \
			echo $$f $$l...   ; \
			rm /tmp/mytst.* || true; \
			./slimfastq -u $$f -f /tmp/mytst -O -l $$l -q && \
			./slimfastq -u /tmp/mytst.fastq -f /tmp/mytst -O -d && \
			tools/mydiff.pl $$f /tmp/mytst.fastq || break ; \
		done || break ; \
	done

test-filer:
	g++ $(FLAGS) -o $@ -g filer.tst.cpp
	@ ./$@ && echo "Pass!" || echo "Fail"

playground:
	@ echo $(filter-out molder.cpp, $(shell echo *.cpp))

install:
ifeq ("$(wildcard ./slimfastq)","")
	@echo "Please compile slimfastq first. You can do it by running:";
	@echo "% make"
	@echo "(optional) %make test"
	@echo "% make install"
	@echo "(Note that 'make slimfastq install' would not work as expected)"
	@false
else
	@install -t /usr/local/bin/ ./slimfastq tools/slimfastq.multi 2>/dev/null \
	|| cp  ./slimfastq tools/slimfastq.multi /usr/local/bin/ \
	|| echo "failed to install, please use ./slimfastq and tools/slimfastq.multi in place, or copy them to your lookup path"
	@echo "\nAll done!"
endif

uninstall:
	rm /usr/local/bin/slimfastq* || /bin/true