├── .clang-format ├── .clang-format-ignore ├── .clang-format-include ├── .clang-tidy ├── .clang-tidy-ignore ├── .clang-tidy-include ├── .codecov.yml ├── .github └── workflows │ ├── build-test.yml │ ├── check-format.yml │ ├── coverage.yml │ └── tidy.yml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── README.md ├── benchmark ├── benchmark-list-wrapper.sh ├── benchmark_main.cc.in ├── data │ ├── benchmark_156.fasta │ ├── benchmark_16k.fasta │ ├── benchmark_1k.fasta │ ├── benchmark_2k.fasta │ ├── benchmark_32k.fasta │ ├── benchmark_4k.fasta │ └── benchmark_8k.fasta ├── libcoati-benchmark-tests.txt └── meson.build ├── coati.sublime-project.in ├── contrib ├── CLI │ └── CLI11.hpp ├── doctest │ └── doctest │ │ └── doctest.h ├── fstlib │ ├── AUTHORS │ ├── COPYING │ ├── compat.cc │ ├── encode.cc │ ├── flags.cc │ ├── fst-types.cc │ ├── fst.cc │ ├── fst │ │ ├── accumulator.h │ │ ├── add-on.h │ │ ├── arc-arena.h │ │ ├── arc-map.h │ │ ├── arc.h │ │ ├── arcfilter.h │ │ ├── arcsort.h │ │ ├── bi-table.h │ │ ├── cache.h │ │ ├── cc-visitors.h │ │ ├── closure.h │ │ ├── compact-fst.h │ │ ├── compat.h │ │ ├── complement.h │ │ ├── compose-filter.h │ │ ├── compose.h │ │ ├── concat.h │ │ ├── connect.h │ │ ├── const-fst.h │ │ ├── determinize.h │ │ ├── dfs-visit.h │ │ ├── difference.h │ │ ├── disambiguate.h │ │ ├── edit-fst.h │ │ ├── encode.h │ │ ├── epsnormalize.h │ │ ├── equal.h │ │ ├── equivalent.h │ │ ├── error-weight.h │ │ ├── expanded-fst.h │ │ ├── expander-cache.h │ │ ├── expectation-weight.h │ │ ├── factor-weight.h │ │ ├── filter-state.h │ │ ├── flags.h │ │ ├── float-weight.h │ │ ├── fst-decl.h │ │ ├── fst.h │ │ ├── fstlib.h │ │ ├── generic-register.h │ │ ├── heap.h │ │ ├── icu.h │ │ ├── impl-to-fst.h │ │ ├── intersect.h │ │ ├── interval-set.h │ │ ├── invert.h │ │ ├── isomorphic.h │ │ ├── label-reachable.h │ │ ├── lexicographic-weight.h │ │ ├── lock.h │ │ ├── log.h │ │ ├── lookahead-filter.h │ │ ├── lookahead-matcher.h │ │ ├── mapped-file.h │ │ ├── matcher-fst.h │ │ ├── matcher.h │ │ ├── memory.h │ │ ├── minimize.h │ │ ├── mutable-fst.h │ │ ├── pair-weight.h │ │ ├── partition.h │ │ ├── power-weight-mappers.h │ │ ├── power-weight.h │ │ ├── product-weight.h │ │ ├── project.h │ │ ├── properties.h │ │ ├── prune.h │ │ ├── push.h │ │ ├── queue.h │ │ ├── randequivalent.h │ │ ├── randgen.h │ │ ├── rational.h │ │ ├── register.h │ │ ├── relabel.h │ │ ├── replace-util.h │ │ ├── replace.h │ │ ├── reverse.h │ │ ├── reweight.h │ │ ├── rmepsilon.h │ │ ├── rmfinalepsilon.h │ │ ├── set-weight.h │ │ ├── shortest-distance.h │ │ ├── shortest-path.h │ │ ├── signed-log-weight.h │ │ ├── sparse-power-weight.h │ │ ├── sparse-tuple-weight.h │ │ ├── state-map.h │ │ ├── state-reachable.h │ │ ├── state-table.h │ │ ├── statesort.h │ │ ├── string-weight.h │ │ ├── string.h │ │ ├── symbol-table-ops.h │ │ ├── symbol-table.h │ │ ├── synchronize.h │ │ ├── test-properties.h │ │ ├── topsort.h │ │ ├── tuple-weight.h │ │ ├── union-find.h │ │ ├── union-weight.h │ │ ├── union.h │ │ ├── util.h │ │ ├── vector-fst.h │ │ ├── verify.h │ │ ├── visit.h │ │ ├── weight.h │ │ └── windows_defs.inc │ ├── mapped-file.cc │ ├── properties.cc │ ├── symbol-table-ops.cc │ ├── symbol-table.cc │ ├── util.cc │ └── weight.cc ├── meson.build └── random │ ├── random.cpp │ └── random.hpp ├── cppcheck_suppressions.txt ├── doc ├── Doxyfile.in └── meson.build ├── gcovr.cfg ├── meson.build ├── meson_options.txt ├── sampledata ├── example-001.fasta ├── example-002.fasta ├── example-003.fasta ├── example-10k.fasta ├── example-160k.fasta ├── example-20k.fasta ├── example-40k.fasta ├── example-80k.fasta ├── example-msa-001.fasta ├── example-msa-001.newick ├── example-msa-002.fasta ├── example-msa-002.newick ├── example-msa-003.fasta └── example-msa-003.newick ├── src ├── coati-alignpair.cc ├── coati-format.cc ├── coati-genseed.cc ├── coati-msa.cc ├── coati-sample.cc ├── coati-version.cc ├── coati.cc.in ├── include │ └── coati │ │ ├── align_fst.hpp │ │ ├── align_marginal.hpp │ │ ├── align_msa.hpp │ │ ├── align_pair.hpp │ │ ├── coati.hpp │ │ ├── data.hpp │ │ ├── dna_syms.hpp │ │ ├── ecm_unrest.tcc │ │ ├── eigen_matrix.hpp │ │ ├── fasta.hpp │ │ ├── format.hpp │ │ ├── insertions.hpp │ │ ├── io.hpp │ │ ├── json.hpp │ │ ├── matrix.hpp │ │ ├── mg94p.tcc │ │ ├── mg94q.tcc │ │ ├── mutation_coati.hpp │ │ ├── mutation_ecm.hpp │ │ ├── mutation_fst.hpp │ │ ├── phylip.hpp │ │ ├── semiring.hpp │ │ ├── structs.hpp │ │ ├── tree.hpp │ │ └── utils.hpp ├── lib │ ├── align_fst.cc │ ├── align_marginal.cc │ ├── align_msa.cc │ ├── align_pair.cc │ ├── fasta.cc │ ├── format.cc │ ├── insertions.cc │ ├── io.cc │ ├── json.cc │ ├── meson.build │ ├── mutation_coati.cc │ ├── mutation_ecm.cc │ ├── mutation_fst.cc │ ├── phylip.cc │ ├── tree.cc │ ├── utils.cc │ └── version.cc ├── meson.build ├── verb.hpp └── version.h.in.in ├── subprojects ├── eigen.wrap ├── google-benchmark.wrap └── json.wrap └── tests ├── doctest-list-wrapper.sh ├── libcoati-doctest-tests.txt ├── libcoati-doctest.cc └── meson.build /.clang-format: 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