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SAMTOOLDIR=/usr/include/samtools
SEQANDIR=/usr/include/seqan
CPPFLAGS+= -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL
CXXFLAGS+= -I$(SAMTOOLDIR) -I$(SEQANDIR) -I./ -Wno-deprecated -O3 -std=gnu++98
LDFLAGS+= -lbam -lz -lboost_program_options -lpthread
SRCSDINDEL=DInDel.cpp HapBlock.cpp HaplotypeDistribution.cpp ObservationModelFB.cpp GetCandidates.cpp Faster.cpp
OBJSDINDEL=$(SRCSDINDEL:%.cpp=%.o)
dindel:$(OBJSDINDEL) Read.hpp DInDel.hpp HapBlock.hpp Haplotype.hpp HaplotypeDistribution.hpp MyBam.hpp GetCandidates.hpp Variant.hpp Fasta.hpp OutputData.hpp MLAlignment.hpp ObservationModelSeqAn.hpp VariantFile.hpp ReadIndelErrorModel.hpp Library.hpp Faster.hpp
$(CXX) -o $@ $(CXXFLAGS) $(DINDELFLAGS) $(OBJSDINDEL) $(LDFLAGS)
clean:
rm -f $(OBJSDINDEL) $(OBJSCOMPAREVARIANTS) $(OBJSMAKEGLF) *.o
distclean: clean
rm -f dindel
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