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208 lines
4.9 KiB
Makefile
208 lines
4.9 KiB
Makefile
#OBJ_DIR = ./
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HEADERS = src/Variant.h \
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src/split.h \
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src/pdflib.hpp \
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src/var.hpp \
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src/cdflib.hpp \
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src/rnglib.hpp \
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src/join.h
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SOURCES = src/Variant.cpp \
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src/rnglib.cpp \
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src/var.cpp \
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src/pdflib.cpp \
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src/cdflib.cpp \
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src/split.cpp
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OBJECTS= $(SOURCES:.cpp=.o)
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VCF_LIB_LOCAL:=$(shell pwd)
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BIN_DIR:=bin
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LIB_DIR:=lib
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SRC_DIR=src
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INC_DIR:=include
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OBJ_DIR:=obj
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LIB = libvcflib.a
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SOVERSION = 1
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SLIB = libvcflib.so.$(SOVERSION)
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# TODO
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#vcfstats.cpp
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BIN_SOURCES = src/vcfecho.cpp \
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src/vcfnormalizesvs.cpp \
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src/dumpContigsFromHeader.cpp \
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src/bFst.cpp \
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src/pVst.cpp \
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src/hapLrt.cpp \
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src/popStats.cpp \
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src/wcFst.cpp \
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src/iHS.cpp \
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src/segmentFst.cpp \
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src/segmentIhs.cpp \
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src/genotypeSummary.cpp \
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src/sequenceDiversity.cpp \
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src/pFst.cpp \
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src/smoother.cpp \
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src/LD.cpp \
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src/plotHaps.cpp \
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src/abba-baba.cpp \
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src/permuteGPAT++.cpp \
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src/permuteSmooth.cpp \
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src/normalize-iHS.cpp \
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src/meltEHH.cpp \
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src/vcfaltcount.cpp \
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src/vcfhetcount.cpp \
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src/vcfhethomratio.cpp \
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src/vcffilter.cpp \
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src/vcf2tsv.cpp \
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src/vcfgenotypes.cpp \
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src/vcfannotategenotypes.cpp \
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src/vcfcommonsamples.cpp \
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src/vcfremovesamples.cpp \
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src/vcfkeepsamples.cpp \
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src/vcfsamplenames.cpp \
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src/vcfgenotypecompare.cpp \
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src/vcffixup.cpp \
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src/vcfclassify.cpp \
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src/vcfsamplediff.cpp \
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src/vcfremoveaberrantgenotypes.cpp \
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src/vcfrandom.cpp \
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src/vcfparsealts.cpp \
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src/vcfstats.cpp \
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src/vcfflatten.cpp \
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src/vcfprimers.cpp \
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src/vcfnumalt.cpp \
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src/vcfcleancomplex.cpp \
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src/vcfintersect.cpp \
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src/vcfannotate.cpp \
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src/vcfallelicprimitives.cpp \
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src/vcfoverlay.cpp \
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src/vcfaddinfo.cpp \
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src/vcfkeepinfo.cpp \
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src/vcfkeepgeno.cpp \
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src/vcfafpath.cpp \
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src/vcfcountalleles.cpp \
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src/vcflength.cpp \
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src/vcfdistance.cpp \
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src/vcfrandomsample.cpp \
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src/vcfentropy.cpp \
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src/vcfglxgt.cpp \
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src/vcfroc.cpp \
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src/vcfcheck.cpp \
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src/vcfstreamsort.cpp \
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src/vcfuniq.cpp \
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src/vcfuniqalleles.cpp \
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src/vcfremap.cpp \
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src/vcf2fasta.cpp \
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src/vcfsitesummarize.cpp \
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src/vcfbreakmulti.cpp \
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src/vcfcreatemulti.cpp \
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src/vcfevenregions.cpp \
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src/vcfcat.cpp \
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src/vcfgenosummarize.cpp \
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src/vcfgenosamplenames.cpp \
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src/vcfgeno2haplo.cpp \
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src/vcfleftalign.cpp \
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src/vcfcombine.cpp \
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src/vcfgeno2alleles.cpp \
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src/vcfindex.cpp \
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src/vcf2dag.cpp \
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src/vcfsample2info.cpp \
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src/vcfqual2info.cpp \
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src/vcfinfo2qual.cpp \
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src/vcfglbound.cpp \
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src/vcfunphase.cpp \
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src/vcfnull2ref.cpp \
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src/vcfinfosummarize.cpp
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# when we can figure out how to build on mac
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# src/vcfsom.cpp
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#BINS = $(BIN_SOURCES:.cpp=)
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BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
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SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
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# Use ?= to allow overriding from the env or command-line.
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MAKE ?= make
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LOCALBASE ?= /usr/local
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LIB_PATH ?= ${LOCALBASE}/lib
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CC ?= cc
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CXX ?= c++
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CXXFLAGS ?= -O3
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CFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC
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CXXFLAGS += $(CFLAGS) --std=c++11
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#CXXFLAGS += -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
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DESTDIR ?= stage
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PREFIX ?= /usr/local
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STRIP ?= strip
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INSTALL ?= install -c
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MKDIR ?= mkdir -p
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AR ?= ar
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SSW = src/ssw.o src/ssw_cpp.o
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INCLUDES = -I${LOCALBASE}/include \
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-I${LOCALBASE}/include/smithwaterman \
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-I${LOCALBASE}/include/multichoose \
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-I${LOCALBASE}/include/fastahack \
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-I${LOCALBASE}/include/intervaltree
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LDFLAGS += -L. -lvcflib \
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-L$(LIB_PATH) -lsw -ltabix -lhts -lfastahack -lfilevercmp \
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-lpthread -lz -lm
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all: $(OBJECTS) $(BINS) $(LIB) $(SLIB)
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ssw.o: src/ssw.h
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ssw_cpp.o: src/ssw_cpp.h
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openmp:
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$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
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profiling:
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$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
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gprof:
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$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
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$(OBJECTS): $(SOURCES) $(HEADERS)
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$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(CXXFLAGS)
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$(SHORTBINS):
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$(MAKE) $(BIN_DIR)/$@
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$(BINS): $(BIN_SOURCES) $(LIB) $(OBJECTS) $(SSW) pre
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$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(CXXFLAGS) $(LDFLAGS)
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$(LIB): $(OBJECTS) $(SSW)
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ar rs $(LIB) $(OBJECTS) $(SSW)
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$(SLIB): $(OBJECTS) $(SSW)
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$(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJECTS) $(SSW)
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install: all
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$(MKDIR) $(DESTDIR)$(PREFIX)/bin
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$(MKDIR) $(DESTDIR)$(PREFIX)/include/vcflib
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$(MKDIR) $(DESTDIR)$(PREFIX)/lib
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$(INSTALL) bin/* $(DESTDIR)$(PREFIX)/bin
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$(INSTALL) src/*.h src/*.hpp $(DESTDIR)$(PREFIX)/include/vcflib
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$(INSTALL) $(LIB) $(SLIB) $(DESTDIR)$(PREFIX)/lib
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install-strip: install
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$(STRIP) $(DESTDIR)$(PREFIX)/bin/* $(DESTDIR)$(PREFIX)/lib/$(SLIB)
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test: $(BINS)
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@prove -Itests/lib -w tests/*.t
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clean:
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rm -f $(BINS) $(OBJECTS)
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rm -f ssw_cpp.o ssw.o
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rm -f $(LIB)
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rm -rf $(BIN_DIR)
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pre:
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mkdir -p $(BIN_DIR)
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.PHONY: clean all test pre
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