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Makefile
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CC = g++
CFLAGS = -O3 -std=c++11 -pthread
SINGLELDFLAGS = -pthread
COMBINERLDFLAGS = -pthread
SINGLE = bartender_single
EXTRACTOR = bartender_extractor
COMBINER = bartender_combiner
SINGLEWRAPPER = bartender_single_com
EXTRACTORWRAPPER = bartender_extractor_com
COMBINERWRAPPER = bartender_combiner_com
INSTALLDIR = /usr/local/bin
# command
RM =rm
CP =cp
CD =cd
MV =mv
BARTENDERSINGLESOURCES = ./src/barcodemutationgenerator.cpp ./src/barcodetabledumper.cpp ./src/centerclustermapper.cpp ./src/centerhistogramgenerator.cpp ./src/centerrecalibrator.cpp ./src/barcodecluster.cpp ./src/clusteralgorithm.cpp ./src/clustercenterlinkgenerator.cpp ./src/clusteringwithtest.cpp ./src/clustermergerpooltester.cpp ./src/clustermergertester.cpp ./src/clustermergerunpooltester.cpp ./src/clusteroutput.cpp ./src/clustersplitter.cpp ./src/clustertabledumper.cpp ./src/distanceselector.cpp ./src/errorrateestimator.cpp ./src/hypothesistester.cpp ./src/idgenerator.cpp ./src/kmers_dictionary.cpp ./src/bartender_single.cpp ./src/meansequentialestimator.cpp ./src/mergebycenters.cpp ./src/mixturebptester.cpp ./src/proportionpooltest.cpp ./src/proportiontest.cpp ./src/qualitytabledumper.cpp ./src/seedselector.cpp ./src/util.cpp ./src/centerclustermapperiterator.cpp ./src/clustermergeronesampletester.cpp ./src/oneproportiontest.cpp ./src/clusterpruner.cpp ./src/meanestimator.cpp ./src/pcrprocessor.cpp ./src/rawbarcodeloader.cpp ./src/barcodepool.cpp ./src/clusteringdriver.cpp ./src/clustersbucketer.cpp ./src/barcodeindexer.cpp ./src/threadwrapper.cpp ./src/clusterThreadBatcher.cpp ./src/barcodepoolstatistics.cpp ./src/errorestimator.cpp ./src/bpfrequencytracker.cpp ./src/entropyseedselector.cpp ./src/jointentropyseedselector.cpp ./src/miseedselector.cpp ./src/pairwisemeasurement.cpp ./src/pairwisemi.cpp ./src/mutualinformationcalculator.cpp ./src/seedpositionpool.cpp ./src/jointentropy.cpp
BARTENDERSINGLEOBJECTS=$(BARTENDERSINGLESOURCES:.cpp=.o)
BARTENDEREXTRACTORSOURCES = ./src/kmerdecoder.cpp ./src/kmers_bitwisetransform.cpp ./src/kmers_dictionary.cpp ./src/sequence.cpp ./src/util.cpp ./src/singlereadsprocessor.cpp ./src/bartender_extractor.cpp ./src/barcodeextractor.cpp ./src/pattern.cpp ./src/fastapattern.cpp ./src/fastqpattern.cpp ./src/UmiExtractor.cpp ./src/SingleReadProcessorWithUmi.cpp
BARTENDEREXTRACTOROBJECTS=$(BARTENDEREXTRACTORSOURCES:.cpp=.o)
COMBINERSOURCES = ./src/bartender_combiner.cpp ./src/kmers_dictionary.cpp ./src/util.cpp ./src/barcodecluster.cpp ./src/clusteroutput.cpp ./src/testSimulation.cpp ./src/multipletimepointsprocessor.cpp ./src/centerclustermapper.cpp ./src/centerclustermapperiterator.cpp ./src/errorrateestimator.cpp ./src/clusterloader.cpp ./src/clustercenterlinkgenerator.cpp ./src/idgenerator.cpp ./src/mergebycenters.cpp ./src/barcodemutationgenerator.cpp ./src/barcodetabledumper.cpp ./src/clustertabledumper.cpp ./src/qualitytabledumper.cpp ./src/barcodepool.cpp ./src/kmers_bitwisetransform.cpp ./src/timepointsmerger.cpp ./src/threadwrapper.cpp
COMBINEROBJECTS = $(COMBINERSOURCES:.cpp=.o)
all: $(BARTENDERSINGLESOURCES) $(SINGLE) $(COMBINER) $(EXTRACTOR)
install:
$(CP) $(SINGLE) $(INSTALLDIR)/
$(CP) $(EXTRACTOR) $(INSTALLDIR)/
$(CP) $(COMBINER) $(INSTALLDIR)/
$(CP) $(SINGLEWRAPPER) $(INSTALLDIR)/
$(CP) $(EXTRACTORWRAPPER) $(INSTALLDIR)/
$(CP) $(COMBINERWRAPPER) $(INSTALLDIR)/
uninstall:
$(RM) -r $(INSTALLDIR)/$(SINGLE)
$(RM) -r $(INSTALLDIR)/$(EXTRACTOR)
$(RM) -r $(INSTALLDIR)/$(SINGLEWRAPPER)
$(RM) -r $(INSTALLDIR)/$(EXTRACTORWRAPPER)
$(RM) -r $(INSTALLDIR)/$(COMBINER)
$(RM) -r $(INSTALLDIR)/$(COMBINERWRAPPER)
clean:
$(RM) $(BARTENDERSINGLEOBJECTS)
$(RM) $(BARTENDEREXTRACTOROBJECTS)
$(RM) $(COMBINEROBJECTS)
$(RM) $(SINGLE)
$(RM) $(EXTRACTOR)
$(RM) $(COMBINER)
$(SINGLE): $(BARTENDERSINGLEOBJECTS)
$(CC) $(BARTENDERSINGLEOBJECTS) -o $@ $(SINGLELDFLAGS)
$(EXTRACTOR): $(BARTENDEREXTRACTOROBJECTS)
$(CC) $(BARTENDEREXTRACTOROBJECTS) -o $@
$(COMBINER): $(COMBINEROBJECTS)
$(CC) $(COMBINEROBJECTS) -o $@ $(COMBINERLDFLAGS)
.cpp.o:
$(CC) -c $(CFLAGS) $< -o $@