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Makefile
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.PHONY: all clean test cpptest converttest verify quick-verify
CXX= g++
CXXFLAGS= -g -Wall -Wno-unused-function -std=c++17 -O2 -I/opt/homebrew/include
LDFLAGS= -lz -lglpk -L/opt/homebrew/lib
LARGEFLAGS= -DLARGE_KMERS
ELARGEFLAGS= -DEXTRA_LARGE_KMERS
SRC= src
TESTS= tests
GTEST= $(TESTS)/googletest/googletest
DATA= data
all: kmercamel
test: cpptest converttest verify
mask-verify:
./verify.py --k 13 --superstring_path $(DATA)/global-k13c.fa $(DATA)/spneumoniae.fa
./verify.py --k 31 --superstring_path $(DATA)/global-k31c.fa $(DATA)/spneumoniae.fa
./verify.py --k 63 --superstring_path $(DATA)/global-k63c.fa $(DATA)/spneumoniae.fa
./verify.py --k 127 --superstring_path $(DATA)/global-k127c.fa $(DATA)/spneumoniae.fa
verify: verify.py kmercamel
./verify.py $(DATA)/spneumoniae.fa
quick-verify: verify.py kmercamel
./verify.py --quick $(DATA)/spneumoniae.fa
cpptest: kmercameltest kmercameltest-large kmercameltest-extra-large
./kmercameltest
./kmercameltest-large
./kmercameltest-extra-large
converttest: convert_superstring_unittest.py
./convert_superstring_unittest.py
kmercamel: $(SRC)/main.cpp $(SRC)/$(wildcard *.cpp *.h *.hpp) src/version.h
./create-version.sh
$(CXX) $(CXXFLAGS) $(SRC)/main.cpp -o $@ $(LDFLAGS)
cp kmercamel 🐫 || true
kmercameltest: $(TESTS)/unittest.cpp gtest-all.o $(SRC)/$(wildcard *.cpp *.h *.hpp) $(TESTS)/$(wildcard *.cpp *.h *.hpp)
$(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include $(TESTS)/unittest.cpp gtest-all.o -pthread -o $@ $(LDFLAGS)
kmercameltest-large: $(TESTS)/unittest.cpp gtest-all.o $(SRC)/$(wildcard *.cpp *.h *.hpp) $(TESTS)/$(wildcard *.cpp *.h *.hpp)
$(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include $(TESTS)/unittest.cpp gtest-all.o -pthread -o $@ $(LDFLAGS) $(LARGEFLAGS)
kmercameltest-extra-large: $(TESTS)/unittest.cpp gtest-all.o $(SRC)/$(wildcard *.cpp *.h *.hpp) $(TESTS)/$(wildcard *.cpp *.h *.hpp)
$(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include $(TESTS)/unittest.cpp gtest-all.o -pthread -o $@ $(LDFLAGS) $(ELARGEFLAGS)
gtest-all.o: $(GTEST)/src/gtest-all.cc $(wildcard *.cpp *.h *.hpp)
$(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include -I $(GTEST) -DGTEST_CREATE_SHARED_LIBRARY=1 -c -pthread $(GTEST)/src/gtest-all.cc -o $@
src/version.h: src/version
./create-version.sh
clean:
rm -f kmercamel
rm -f 🐫 || true
rm -f kmercameltest
rm -f kmercameltest-large
rm -r -f ./bin
rm -f gtest-all.o
rm -f src/version.h