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..
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CMakeLists.txt
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CacheFriendlyOperations.cpp
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CacheFriendlyOperations.h
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ExtendedSubstitutionMatrix.cpp
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ExtendedSubstitutionMatrix.h
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IndexBuilder.cpp
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IndexBuilder.h
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IndexTable.h
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Indexer.cpp
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Indexer.h
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KmerGenerator.cpp
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KmerGenerator.h
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Main.cpp
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Prefiltering.cpp
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Prefiltering.h
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PrefilteringIndexReader.cpp
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PrefilteringIndexReader.h
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QueryMatcher.cpp
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QueryMatcher.h
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ReducedMatrix.cpp
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ReducedMatrix.h
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SequenceLookup.cpp
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SequenceLookup.h
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UngappedAlignment.cpp
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UngappedAlignment.h
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ungappedprefilter.cpp
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