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Makefile
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# Example command to build: make all -j9 && make deploy
release = debarcode uvc-1-fopenmp-thread uvc-1-cpp-std-thread
release : $(release)
debug = debarcode uvc-2-fopenmp-thread-asan.debug uvc-2-cpp-std-thread-asan.debug uvc-3-asan.debug uvc-4.debug
debug : $(debug)
debug-ub : debarcode uvc-2-fopenmp-thread-ubsan.debug uvc-2-cpp-std-thread-ubsan.debug uvc-3-ubsan.debug
all : release debug
ALL : all debug-ub
HDR=CLI11-1.7.1/CLI11.hpp Hash.hpp main_conversion.hpp main_consensus.hpp \
CmdLineArgs.hpp common.hpp grouping.hpp iohts.hpp logging.hpp main.hpp MolecularID.hpp version.h
SRC=CmdLineArgs.cpp common.cpp grouping.cpp iohts.cpp logging.cpp main.cpp MolecularID.cpp version.cpp
DEP=bcf_formats.step1.hpp instcode.hpp Makefile
HTSPATH=ext/htslib-1.11-lowdep/libhts.a
HTSFLAGS=$(HTSPATH) -I ext/htslib-1.11-lowdep/ -pthread -lm -lz -lbz2 -llzma # -lcurl -lcrypto # can be changed depending on the specific installed components of htslib (please refer to the INSTALL file in htslib)
CC=gcc # can be changed to clang or other compilers as needed
CXX=g++ # can be changed to clang or other compilers as needed
CXXFLAGS=-std=c++14 -static-libstdc++ -Wall
COMMIT_VERSION=$(shell git rev-parse HEAD | head -c 7)
COMMIT_DIFF_SH=$(shell git diff HEAD --shortstat)
COMMIT_DIFF_FULL=$(shell echo "R\"ZXF_specQUOTE(\n $$(git diff HEAD | sed 's/ZXF_specQUOTE/ZXF_specquote/g') \n)ZXF_specQUOTE\"" > gitdiff.txt)
VERFLAGS=-DCOMMIT_VERSION="\"$(COMMIT_VERSION)\"" -DCOMMIT_DIFF_SH="\"$(COMMIT_DIFF_SH)\"" -DCOMMIT_DIFF_FULL="\"$(COMMIT_DIFF_FULL)\""
# UVC_IN_DEBUG_MODE enables locus-specific diagnostic debugging info
DEBUG_OPTS=-DUVC_IN_DEBUG_MODE -static-libasan
UBSAN=--param=max-vartrack-size=640000000 -fsanitize=undefined
debarcode : debarcode_main.c version.h Makefile
$(CC) -O3 -o debarcode $(VERFLAGS) debarcode_main.c ${HTSFLAGS}
# the main executable, uses OpenMP for multi-threading
uvc-1-fopenmp-thread : $(HDR) $(SRC) $(DEP)
$(CXX) -O3 -DNDEBUG -o uvc-1-fopenmp-thread $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) -fopenmp # -l htslib
# the main executable, uses C++ standard template library thread for multi-threading, useful if OpenMP runtime is not available
uvc-1-cpp-std-thread : $(HDR) $(SRC) $(DEP)
$(CXX) -O3 -DNDEBUG -o uvc-1-cpp-std-thread $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) -DUSE_STDLIB_THREAD # -l htslib
uvc-2-fopenmp-thread-asan.debug : $(HDR) $(SRC) $(DEP)
$(CXX) -O2 -g -p -o uvc-2-fopenmp-thread-asan.debug $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) $(DEBUG_OPTS) -fopenmp -fsanitize=address
uvc-2-fopenmp-thread-ubsan.debug : $(HDR) $(SRC) $(DEP)
$(CXX) -O2 -g -p -o uvc-2-fopenmp-thread-ubsan.debug $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) $(DEBUG_OPTS) -fopenmp $(UBSAN)
uvc-2-cpp-std-thread-asan.debug : $(HDR) $(SRC) $(DEP)
$(CXX) -O2 -g -p -o uvc-2-cpp-std-thread-asan.debug $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) $(DEBUG_OPTS) -DUSE_STDLIB_THREAD -fsanitize=address
uvc-2-cpp-std-thread-ubsan.debug : $(HDR) $(SRC) $(DEP)
$(CXX) -O2 -g -p -o uvc-2-cpp-std-thread-ubsan.debug $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) $(DEBUG_OPTS) -DUSE_STDLIB_THREAD $(UBSAN)
uvc-3-asan.debug : $(HDR) $(SRC) $(DEP)
$(CXX) -O2 -g -p -o uvc-3-asan.debug $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) $(DEBUG_OPTS) -fsanitize=address
uvc-3-ubsan.debug : $(HDR) $(SRC) $(DEP)
$(CXX) -O2 -g -p -o uvc-3-ubsan.debug $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) $(DEBUG_OPTS) $(UBSAN)
uvc-4.debug : $(HDR) $(SRC) $(DEP)
$(CXX) -O0 -g -p -o uvc-4.debug $(CXXFLAGS) $(VERFLAGS) $(SRC) $(HTSFLAGS) $(DEBUG_OPTS) -Wextra -DENABLE_ASSERT_IN_UVC
bcf_formats_generator1.out : bcf_formats_generator1.cpp version.h
$(CXX) -o bcf_formats_generator1.out $(CXXFLAGS) bcf_formats_generator1.cpp
bcf_formats.step1.hpp : bcf_formats_generator1.out
./bcf_formats_generator1.out > bcf_formats.step1.hpp # auto-generate the C++ code from the BCF-template generator
.PHONY: release all debug debug-ub ALL clean deploy
clean:
rm bcf_formats_generator1.out bcf_formats.step1.hpp *.o *.debug uvc-1-fopenmp-thread uvc-1-cpp-std-thread *.gch debarcode || true
deploy:
cp uvc-1-fopenmp-thread bin/uvc1 # The default binary executable uses OpenML thread, and uvc1 is used by uvcTN.sh
cp $(release) bin/ || true
cp $(debug) bin/ || true