├── .gitignore ├── BPR2 ├── .gitignore ├── AUTHORS ├── COPYING ├── ChangeLog ├── INSTALL ├── Makefile.am ├── Makefile.in ├── Makefile.init ├── NEWS ├── README ├── aclocal.m4 ├── autom4te.cache │ ├── output.0 │ ├── output.1 │ ├── requests │ ├── traces.0 │ └── traces.1 ├── bootstrap.sh ├── config.log ├── config.status ├── config │ ├── compile │ ├── config.guess │ ├── config.sub │ ├── depcomp │ ├── install-sh │ ├── kbs.m4 │ ├── libtool.m4 │ ├── ltmain.sh │ ├── missing │ └── mkinstalldirs ├── configure ├── configure.in ├── doxyBpr.cfg ├── libtool └── src │ ├── .deps │ └── fibstring-fib.main.Po │ ├── Extern │ ├── .deps │ │ └── libextern_la-randomlib.Plo │ ├── Makefile.am │ ├── Makefile.in │ ├── randomlib.c │ └── randomlib.h │ ├── Main │ ├── .deps │ │ ├── bprtime-bprtime.main.Po │ │ ├── fibstring-fib.main.Po │ │ └── periodicstr-periodicStrGen.main.Po │ ├── .kdbgrc.bktref │ ├── .kdbgrc.bprtime │ ├── .kdbgrc.makeclusteredsft │ ├── .kdbgrc.periodicstr │ ├── Makefile.am │ ├── Makefile.in │ ├── bprtime.main.c │ ├── fib.main.c │ └── periodicStrGen.main.c │ ├── Makefile.am │ ├── Makefile.in │ ├── Standard │ ├── .deps │ │ ├── libstandard_la-kbs_Alphabet.Plo │ │ ├── libstandard_la-kbs_Error.Plo │ │ ├── libstandard_la-kbs_Math.Plo │ │ ├── libstandard_la-kbs_String.Plo │ │ └── libstandard_la-kbs_Time.Plo │ ├── Makefile.am │ ├── Makefile.in │ ├── kbs_Alphabet.c │ ├── kbs_Alphabet.h │ ├── kbs_Error.c │ ├── kbs_Error.h │ ├── kbs_Limits.h │ ├── kbs_Math.c │ ├── kbs_Math.h │ ├── kbs_String.c │ ├── kbs_String.h │ ├── kbs_Time.c │ ├── kbs_Time.h │ └── kbs_Types.h │ ├── SuffixArray │ ├── .deps │ │ ├── libsuffixarray_la-kbs_SuffixArray.Plo │ │ ├── libsuffixarray_la-kbs_SuffixArrayAnnotated.Plo │ │ ├── libsuffixarray_la-kbs_SuffixArrayChecker.Plo │ │ └── libsuffixarray_la-kbs_SuffixArrayConstDStepAndPre.Plo │ ├── Makefile.am │ ├── Makefile.in │ ├── kbs_SuffixArray.c │ ├── kbs_SuffixArray.h │ ├── kbs_SuffixArrayAnnotated.c │ ├── kbs_SuffixArrayAnnotated.h │ ├── kbs_SuffixArrayChecker.c │ ├── kbs_SuffixArrayChecker.h │ ├── kbs_SuffixArrayConstDStepAndPre.c │ └── kbs_SuffixArrayConstDStepAndPre.h │ ├── Util │ ├── .deps │ │ ├── libutil_la-kbs_FibonacciString.Plo │ │ ├── libutil_la-kbs_RandomString.Plo │ │ └── libutil_la-kbs_RandomStringFile.Plo │ ├── Makefile.am │ ├── Makefile.in │ ├── kbs_FibonacciString.c │ ├── kbs_FibonacciString.h │ ├── kbs_RandomString.c │ ├── kbs_RandomString.h │ ├── kbs_RandomStringFile.c │ └── kbs_RandomStringFile.h │ ├── config.h │ ├── config.h.in │ └── stamp-h1 ├── DC3 ├── drittel.C ├── tryall.C └── util.h ├── README.md ├── deep-shallow ├── .gitignore ├── COPYRIGHT.GPL.txt ├── COPYRIGHT.MPL.txt ├── Makefile ├── README ├── blind2.c ├── bwt.c ├── bwt_aux.c ├── bwt_aux.h ├── common.h ├── deep2.c ├── ds.c ├── ds_ssort.h ├── globals.c ├── helped.c ├── lcp_aux.c ├── lcp_aux.h ├── shallow.c ├── suftest2.c ├── testlcp.c └── unbwt.c ├── gsa-is ├── .gitignore ├── LICENSE ├── README.md ├── experiments │ ├── Makefile │ ├── README.md │ ├── dataset │ │ ├── input-10000.txt │ │ ├── input-10000.txt.bwt │ │ ├── proteins-10000.fasta │ │ └── reads-10000.fastq │ ├── external │ │ ├── bitvector │ │ │ ├── Makefile │ │ │ ├── lib │ │ │ │ ├── document_array.cpp │ │ │ │ ├── document_array.hpp │ │ │ │ ├── utils.cpp │ │ │ │ ├── utils.hpp │ │ │ │ ├── utils_32.hpp │ │ │ │ └── utils_64.hpp │ │ │ └── main.cpp │ │ ├── malloc_count │ │ │ ├── README.md │ │ │ ├── malloc_count.c │ │ │ ├── malloc_count.h │ │ │ ├── memprofile.h │ │ │ ├── stack_count.c │ │ │ ├── stack_count.h │ │ │ ├── test-malloc_count │ │ │ │ ├── Makefile │ │ │ │ └── test.c │ │ │ └── test-memprofile │ │ │ │ ├── Makefile │ │ │ │ ├── memprofile.gnuplot │ │ │ │ ├── memprofile.pdf │ │ │ │ └── test.cc │ │ ├── sa-is │ │ │ ├── main.cpp │ │ │ ├── makefile │ │ │ ├── readme.txt │ │ │ ├── rel │ │ │ ├── sais │ │ │ └── sais.cpp │ │ └── saca-k │ │ │ ├── input.txt │ │ │ ├── main.cpp │ │ │ ├── makefile │ │ │ ├── readme.txt │ │ │ ├── saca-k │ │ │ └── saca-k.cpp │ ├── lib │ │ ├── document_array.c │ │ ├── document_array.h │ │ ├── file.c │ │ ├── file.h │ │ ├── lcp_array.c │ │ ├── lcp_array.h │ │ ├── suffix_array.c │ │ ├── suffix_array.h │ │ ├── utils.c │ │ └── utils.h │ ├── main.c │ └── scripts │ │ └── downloads.txt ├── gsacak.c ├── gsacak.h ├── gsais.c ├── gsais.h └── test.c ├── gsaca ├── .gitignore ├── LICENSE ├── README.md ├── benchmark │ ├── Makefile │ ├── README │ ├── data │ │ ├── README │ │ ├── largecorpus │ │ │ └── Makefile │ │ ├── pizzachilicorpus │ │ │ └── Makefile │ │ ├── repcorpus │ │ │ └── Makefile │ │ └── silesiacorpus │ │ │ └── Makefile │ ├── dc3 │ │ ├── dc3.C │ │ └── dc3.h │ ├── divsufsort │ │ ├── LICENSE │ │ ├── config.h │ │ ├── divsufsort.c │ │ ├── divsufsort.h │ │ ├── divsufsort_private.h │ │ ├── sssort.c │ │ ├── trsort.c │ │ └── utils.c │ ├── gsaca │ │ ├── gsaca.c │ │ └── gsaca.h │ ├── ka │ │ ├── BooleanString.cpp │ │ ├── BooleanString.h │ │ ├── LinearSuffixSort.cpp │ │ ├── LinearSuffixSort.h │ │ ├── Makefile │ │ ├── orig │ │ │ └── LinearSA.tar │ │ └── suftest.cpp │ ├── programlib │ │ ├── benchmark.cpp │ │ ├── constructsa.cpp │ │ └── corpusbenchmark.sh │ └── sais-lite-2.4.1 │ │ ├── COPYING │ │ ├── Makefile │ │ ├── README │ │ ├── is_orig.c │ │ ├── sais.c │ │ ├── sais.h │ │ ├── sais.hxx │ │ ├── suftest.c │ │ └── test.c ├── gsaca.c └── gsaca.h ├── libdivsufsort ├── .gitignore ├── CHANGELOG.md ├── CMakeLists.txt ├── CMakeModules │ ├── AppendCompilerFlags.cmake │ ├── CheckFunctionKeywords.cmake │ ├── CheckLFS.cmake │ ├── ProjectCPack.cmake │ └── cmake_uninstall.cmake.in ├── LICENSE ├── README.md ├── VERSION.cmake ├── examples │ ├── CMakeLists.txt │ ├── bwt.c │ ├── mksary.c │ ├── sasearch.c │ ├── suftest.c │ └── unbwt.c ├── include │ ├── CMakeLists.txt │ ├── config.h.cmake │ ├── divsufsort.h.cmake │ ├── divsufsort_private.h │ └── lfs.h.cmake ├── lib │ ├── CMakeLists.txt │ ├── divsufsort.c │ ├── sssort.c │ ├── trsort.c │ └── utils.c └── pkgconfig │ ├── CMakeLists.txt │ └── libdivsufsort.pc.cmake ├── msufsort ├── LICENSE ├── SConstruct └── src │ ├── SConscript │ ├── executable │ ├── SConscript │ └── msufsort │ │ ├── SConscript │ │ └── main.cpp │ ├── include │ ├── endian.h │ ├── endian │ │ ├── byte_swap.h │ │ ├── endian.h │ │ ├── endian_swap.h │ │ └── endian_type.h │ └── type_traits │ │ ├── enable_if_integral.h │ │ ├── enable_if_integral_or_enum.h │ │ ├── is_endian.h │ │ ├── opposite_endian.h │ │ └── remove_endian.h │ └── library │ ├── SConscript │ ├── msufsort.h │ └── msufsort │ ├── SConscript │ ├── msufsort.cpp │ └── msufsort.h ├── qsufsort ├── .gitignore ├── Makefile ├── qsufsort.c └── suftest.c ├── sa-ds ├── .gitignore ├── core.cpp ├── is.cpp ├── is.sln ├── is.suo ├── is.vcproj ├── makefile └── readme.txt ├── sa-is ├── .gitignore ├── main.cpp ├── makefile ├── readme.txt └── sais.cpp ├── saca-k ├── .gitignore ├── main.cpp ├── makefile ├── readme.txt └── saca-k.cpp └── sais-lite ├── .gitignore ├── COPYING ├── Makefile ├── README ├── is_orig.c ├── sais.c ├── sais.h ├── sais.hxx ├── suftest.c └── test.c /.gitignore: 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