├── .gitmodules ├── CMakeLists.txt ├── CMakeModules ├── ConfigureCompilerClang.cmake └── ConfigureCompilerGcc.cmake ├── LICENSE ├── README.md ├── include ├── CMakeLists.txt ├── PFP-algos │ ├── CMakeLists.txt │ ├── circpfp-gca.cpp │ ├── circpfp-gca.hpp │ ├── circpfp.cpp │ ├── circpfp.hpp │ ├── circpfpd.cpp │ ├── circpfpd.hpp │ ├── circpfpmw.cpp │ └── circpfpmw.hpp ├── common │ ├── common.hpp │ ├── kseq.h │ ├── utils.c │ ├── utils.h │ ├── xerrors.c │ └── xerrors.h ├── csais │ ├── csais.cpp │ └── csais.h └── eBWT-algos │ ├── CMakeLists.txt │ ├── dictionary.hpp │ ├── ebwt.cpp │ ├── invertebwt.cpp │ ├── parse-gca.cpp │ ├── parse-gca.hpp │ ├── parse.cpp │ ├── parse.hpp │ ├── pfp.hpp │ ├── pfp_ebwt_gca.hpp │ ├── pfp_ebwt_gca_complete.hpp │ ├── pfp_parse-gca.hpp │ └── pfp_parse.hpp ├── pfpebwt ├── thirdparty └── CMakeLists.txt └── yeast.fasta /.gitmodules: -------------------------------------------------------------------------------- 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