├── .gitignore ├── .gitmodules ├── .travis.yml ├── .ycm_extra_conf.py ├── CMakeLists.txt ├── LICENSE ├── README.md ├── codecov.yml ├── conf └── travis-install-mpi.sh ├── ext ├── README.md ├── cxx-prettyprint │ └── prettyprint.hpp ├── libdivsufsort │ ├── AUTHORS │ ├── CMakeLists.txt │ ├── CMakeModules │ │ ├── AppendCompilerFlags.cmake │ │ ├── CheckFunctionKeywords.cmake │ │ ├── CheckLFS.cmake │ │ ├── ProjectCPack.cmake │ │ └── cmake_uninstall.cmake.in │ ├── COPYING │ ├── ChangeLog │ ├── ChangeLog.old │ ├── INSTALL │ ├── Makefile.am │ ├── Makefile.in │ ├── NEWS │ ├── README │ ├── VERSION │ ├── aclocal.m4 │ ├── config │ │ ├── config.guess │ │ ├── config.sub │ │ ├── depcomp │ │ ├── install-sh │ │ ├── ltmain.sh │ │ └── missing │ ├── configure │ ├── configure.ac │ ├── examples │ │ ├── CMakeLists.txt │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── bwt.c │ │ ├── mksary.c │ │ ├── sasearch.c │ │ ├── suftest.c │ │ └── unbwt.c │ ├── include │ │ ├── CMakeLists.txt │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── config.h.cmake │ │ ├── config.h.in │ │ ├── divsufsort.h.cmake │ │ ├── divsufsort64.h.in │ │ ├── divsufsort_private.h │ │ └── lfs.h.cmake │ ├── lib │ │ ├── CMakeLists.txt │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── divsufsort.c │ │ ├── libdivsufsort.sym │ │ ├── libdivsufsort64.sym │ │ ├── sssort.c │ │ ├── trsort.c │ │ └── utils.c │ ├── m4 │ │ ├── libtool.m4 │ │ ├── ltoptions.m4 │ │ ├── ltsugar.m4 │ │ ├── ltversion.m4 │ │ └── lt~obsolete.m4 │ └── pkgconfig │ │ ├── CMakeLists.txt │ │ └── libdivsufsort.pc.cmake └── tclap │ ├── Arg.h │ ├── ArgException.h │ ├── ArgTraits.h │ ├── COPYING │ ├── CmdLine.h │ ├── CmdLineInterface.h │ ├── CmdLineOutput.h │ ├── Constraint.h │ ├── DocBookOutput.h │ ├── HelpVisitor.h │ ├── IgnoreRestVisitor.h │ ├── Makefile.am │ ├── Makefile.in │ ├── MultiArg.h │ ├── MultiSwitchArg.h │ ├── OptionalUnlabeledTracker.h │ ├── StandardTraits.h │ ├── StdOutput.h │ ├── SwitchArg.h │ ├── UnlabeledMultiArg.h │ ├── UnlabeledValueArg.h │ ├── ValueArg.h │ ├── ValuesConstraint.h │ ├── VersionVisitor.h │ ├── Visitor.h │ ├── XorHandler.h │ └── ZshCompletionOutput.h ├── include ├── alphabet.hpp ├── ansv.hpp ├── ansv_common.hpp ├── ansv_merge.hpp ├── bitops.hpp ├── bucketing.hpp ├── bulk_permute.hpp ├── bulk_rma.hpp ├── check_suffix_array.hpp ├── check_suffix_tree.hpp ├── desa.hpp ├── divsufsort_wrapper.hpp ├── dstrings.hpp ├── dvector.hpp ├── generalized_suffix_array.hpp ├── idxsort.hpp ├── kmer.hpp ├── lcp.hpp ├── lookup_table.hpp ├── par_rmq.hpp ├── partition.hpp ├── rmq.hpp ├── seq_query.hpp ├── shifting.hpp ├── stringset.hpp ├── suffix_array.hpp ├── suffix_tree.hpp └── tldt.hpp ├── pbs_ansv.sh ├── pbs_run.sh ├── src ├── CMakeLists.txt ├── benchmark.cpp ├── benchmark_ansv.cpp ├── benchmark_k.cpp ├── desa_main.cpp ├── dss.cpp ├── gsac.cpp ├── kmer_partition.cpp ├── mkpattern.cpp ├── print64.cpp ├── psac.cpp ├── psac_vs_dss.cpp ├── test_slcp.cpp └── tldt.cpp └── test ├── CMakeLists.txt ├── test_ansv.cpp ├── test_bitops.cpp ├── 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