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Makefile
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TARGETS=variantstore test_graphcontainer test_variantgraph test_index test_query bm_query
ifdef D
DEBUG=-g -DDEBUG_MODE
OPT=
else
DEBUG=
OPT=-Ofast
endif
ifdef NH
ARCH=
else
ARCH=-msse4.2 -D__SSE4_2_
endif
ifdef P
PROFILE=-pg -no-pie # for bug in gprof.
endif
CXX = g++ -std=c++17
CC = gcc -std=gnu11
LD= g++ -std=c++17
dot= dot -Grankdir=LR -Tpng
LOC_INCLUDE=include
LOC_LIB=lib
LOC_SRC=src
OBJDIR=obj
SER=ser
CXXFLAGS += -Wall $(DEBUG) $(PROFILE) $(OPT) $(ARCH) -fopenmp -m64 -I. -I$(LOC_INCLUDE)
CFLAGS += -Wall $(DEBUG) $(PROFILE) $(OPT) $(ARCH) -m64 -I. -I$(LOC_INCLUDE)
LDFLAGS += $(DEBUG) $(PROFILE) $(OPT) -L$(LOC_LIB) -lm -lvcflib -lhts -lz \
-lbz2 -llzma -lpthread -lsdsl \
`pkg-config --cflags --libs protobuf` -ltcmalloc
#
# declaration of dependencies
#
all: variantstore
tests: test_graphcontainer test_variantgraph test_index test_query
bm: bm_query
graph: $(SER)/graph.png
# dependencies between programs and .o files
variantstore: $(OBJDIR)/variantstore.o $(OBJDIR)/variantstore_fs.o \
$(OBJDIR)/commands.o \
$(OBJDIR)/variantgraphvertex.pb.o $(OBJDIR)/gqf.o \
$(OBJDIR)/gqf_file.o $(OBJDIR)/rank_select.o \
$(OBJDIR)/hashutil.o $(OBJDIR)/util.o
test_graphcontainer: $(OBJDIR)/test_graphcontainer.o $(OBJDIR)/gqf.o \
$(OBJDIR)/gqf_file.o $(OBJDIR)/rank_select.o \
$(OBJDIR)/hashutil.o $(OBJDIR)/util.o
test_variantgraph: $(OBJDIR)/test_variantgraph.o $(OBJDIR)/variantstore_fs.o\
$(OBJDIR)/variantgraphvertex.pb.o $(OBJDIR)/gqf.o \
$(OBJDIR)/gqf_file.o $(OBJDIR)/rank_select.o \
$(OBJDIR)/hashutil.o $(OBJDIR)/util.o
test_index: $(OBJDIR)/test_index.o $(OBJDIR)/variantstore_fs.o\
$(OBJDIR)/variantgraphvertex.pb.o $(OBJDIR)/gqf.o \
$(OBJDIR)/gqf_file.o $(OBJDIR)/rank_select.o \
$(OBJDIR)/hashutil.o $(OBJDIR)/util.o
test_query: $(OBJDIR)/test_query.o $(OBJDIR)/variantstore_fs.o\
$(OBJDIR)/variantgraphvertex.pb.o $(OBJDIR)/gqf.o \
$(OBJDIR)/gqf_file.o $(OBJDIR)/rank_select.o \
$(OBJDIR)/hashutil.o $(OBJDIR)/util.o
bm_query: $(OBJDIR)/bm_query.o $(OBJDIR)/variantstore_fs.o\
$(OBJDIR)/variantgraphvertex.pb.o $(OBJDIR)/gqf.o \
$(OBJDIR)/gqf_file.o $(OBJDIR)/rank_select.o \
$(OBJDIR)/hashutil.o $(OBJDIR)/util.o
# dependencies between .o files and .cc (or .c) files
$(OBJDIR)/variantstore.o: $(LOC_SRC)/variantstore.cc
$(OBJDIR)/commands.o: $(LOC_SRC)/commands.cc \
$(LOC_INCLUDE)/variant_graph.h \
$(LOC_INCLUDE)/query.h \
$(LOC_INCLUDE)/index.h \
$(LOC_INCLUDE)/variantgraphvertex.pb.h \
$(LOC_INCLUDE)/variantstore_fs.h \
$(LOC_INCLUDE)/graph.h \
$(LOC_INCLUDE)/stream.hpp
$(OBJDIR)/test_graphcontainer.o: $(LOC_SRC)/test_graphcontainer.cc \
$(LOC_INCLUDE)/gqf_cpp.h \
$(LOC_INCLUDE)/graph.h
$(OBJDIR)/test_variantgraph.o: $(LOC_SRC)/test_variantgraph.cc \
$(LOC_INCLUDE)/variant_graph.h \
$(LOC_INCLUDE)/variantgraphvertex.pb.h \
$(LOC_INCLUDE)/variantstore_fs.h \
$(LOC_INCLUDE)/graph.h \
$(LOC_INCLUDE)/dot_graph.h \
$(LOC_INCLUDE)/stream.hpp
$(OBJDIR)/test_index.o: $(LOC_SRC)/test_index.cc \
$(LOC_INCLUDE)/index.h \
$(LOC_INCLUDE)/query.h \
$(LOC_INCLUDE)/variant_graph.h \
$(LOC_INCLUDE)/variantgraphvertex.pb.h \
$(LOC_INCLUDE)/variantstore_fs.h \
$(LOC_INCLUDE)/graph.h
$(OBJDIR)/test_query.o: $(LOC_SRC)/test_query.cc \
$(LOC_INCLUDE)/query.h \
$(LOC_INCLUDE)/index.h \
$(LOC_INCLUDE)/variant_graph.h \
$(LOC_INCLUDE)/variantgraphvertex.pb.h \
$(LOC_INCLUDE)/variantstore_fs.h \
$(LOC_INCLUDE)/graph.h
$(OBJDIR)/bm_query.o: $(LOC_SRC)/bm_query.cc \
$(LOC_INCLUDE)/index.h \
$(LOC_INCLUDE)/variant_graph.h \
$(LOC_INCLUDE)/variantgraphvertex.pb.h \
$(LOC_INCLUDE)/variantstore_fs.h \
$(LOC_INCLUDE)/graph.h
$(OBJDIR)/variantgraphvertex.pb.o: $(LOC_SRC)/variantgraphvertex.pb.cc \
$(LOC_INCLUDE)/variantgraphvertex.pb.h
$(OBJDIR)/gqf.o: $(LOC_SRC)/gqf/gqf.c $(LOC_INCLUDE)/gqf/gqf.h
$(OBJDIR)/gqf_file.o: $(LOC_SRC)/gqf/gqf_file.c $(LOC_INCLUDE)/gqf/gqf_file.h
$(OBJDIR)/hashutil.o: $(LOC_INCLUDE)/gqf/hashutil.h
$(OBJDIR)/rank_select.o: $(LOC_INCLUDE)/gqf/rank_select.h
# create dot graph
$(SER)/graph.png: $(SER)/graph.dot
# generate proto files
proto:
protoc --cpp_out=./ ./include/variantgraphvertex.proto && \
mv include/variantgraphvertex.pb.cc src
#
# generic build rules
#
$(TARGETS):
$(LD) $^ $(LDFLAGS) -o $@
$(OBJDIR)/%.o: $(LOC_SRC)/%.cc | $(OBJDIR)
$(CXX) $(CXXFLAGS) $(INCLUDE) -c -o $@ $<
$(OBJDIR)/%.o: $(LOC_SRC)/%.c | $(OBJDIR)
$(CXX) $(CFLAGS) $(INCLUDE) -c -o $@ $<
$(OBJDIR)/%.o: $(LOC_SRC)/gqf/%.c | $(OBJDIR)
$(CXX) $(CFLAGS) $(INCLUDE) -c -o $@ $<
$(SER)/%.png: $(SER)/%.dot | $(SER)
$(dot) -o $@ $<
$(OBJDIR):
@mkdir -p $(OBJDIR)
$(SER):
@mkdir -p $(SER)
clean:
rm -rf $(OBJDIR) $(SER)/graph.png core $(TARGETS)