├── .github └── workflows │ ├── ci.yml │ └── release.yml ├── .gitignore ├── CHANGELOG.md ├── Cargo.lock ├── Cargo.toml ├── LICENSE-MIT ├── README.md ├── figures ├── bench.png └── sim.png ├── winsfs-cli ├── CHANGELOG.md ├── Cargo.toml ├── LICENSE-MIT ├── src │ ├── cli.rs │ ├── estimate.rs │ ├── estimate │ │ ├── format.rs │ │ ├── logging.rs │ │ └── stopping.rs │ ├── input.rs │ ├── input │ │ ├── saf.rs │ │ └── sfs.rs │ ├── log_likelihood.rs │ ├── main.rs │ ├── shuffle.rs │ ├── split.rs │ ├── stat.rs │ ├── utils.rs │ └── view.rs └── tests │ ├── data │ ├── A-B-C.npy │ ├── A-B-C.sfs │ ├── A-B.npy │ ├── A-B.sfs │ ├── A.npy │ ├── A.saf.gz │ ├── A.saf.idx │ ├── A.saf.pos.gz │ ├── A.sfs │ ├── B.saf.gz │ ├── B.saf.idx │ ├── B.saf.pos.gz │ ├── C.saf.gz │ ├── C.saf.idx │ ├── C.saf.pos.gz │ ├── D-E-F.sfs │ ├── D-E.sfs │ ├── D.banded.saf.gz │ ├── D.banded.saf.idx │ ├── D.banded.saf.pos.gz │ ├── D.sfs │ ├── E.banded.saf.gz │ ├── E.banded.saf.idx │ ├── E.banded.saf.pos.gz │ ├── F.banded.saf.gz │ ├── F.banded.saf.idx │ └── F.banded.saf.pos.gz │ ├── expected │ ├── test_1d_banded_estimate_default.stderr │ ├── test_1d_banded_estimate_default.stdout │ ├── test_1d_banded_log_likelihood.stderr │ ├── test_1d_banded_log_likelihood.stdout │ ├── test_1d_estimate_default.stderr │ ├── test_1d_estimate_default.stdout │ ├── test_1d_estimate_uneven_block_size.stderr │ ├── test_1d_estimate_uneven_block_size.stdout │ ├── test_1d_log_likelihood.stderr │ ├── test_1d_log_likelihood.stdout │ ├── test_1d_stream_banded_estimate_default.stderr │ ├── test_1d_stream_banded_estimate_default.stdout │ ├── test_1d_stream_estimate_default.stderr │ ├── test_1d_stream_estimate_default.stdout │ ├── test_1d_view_fold_from_stdin.stderr │ ├── test_1d_view_fold_from_stdin.stdout │ ├── test_1d_view_fold_normalise.stderr │ ├── test_1d_view_fold_normalise.stdout │ ├── test_1d_view_npy_from_stdin.stderr │ ├── test_1d_view_npy_from_stdin.stdout │ ├── test_2d_banded_estimate_10_epochs.stderr │ ├── test_2d_banded_estimate_10_epochs.stdout │ ├── test_2d_banded_log_likelihood.stderr │ ├── test_2d_banded_log_likelihood.stdout │ ├── test_2d_estimate_default.stderr │ ├── test_2d_estimate_default.stdout │ ├── test_2d_log_likelihood.stderr │ ├── test_2d_log_likelihood.stdout │ ├── test_2d_stream_banded_estimate_3_epochs.stderr │ ├── test_2d_stream_banded_estimate_3_epochs.stdout │ ├── test_2d_stream_estimate_3_epochs.stderr │ ├── test_2d_stream_estimate_3_epochs.stdout │ ├── test_2d_view_fold_npy.stderr │ ├── test_2d_view_fold_npy.stdout │ ├── test_2d_view_normalise_from_stdin.stderr │ ├── test_2d_view_normalise_from_stdin.stdout │ ├── test_2d_view_output_npy.stderr │ ├── test_2d_view_output_npy.stdout │ ├── test_3d_banded_estimate_3_epochs.stderr │ ├── test_3d_banded_estimate_3_epochs.stdout │ ├── test_3d_banded_log_likelihood.stderr │ ├── test_3d_banded_log_likelihood.stdout │ ├── test_3d_estimate_3_epochs.stderr │ ├── test_3d_estimate_3_epochs.stdout │ ├── test_3d_log_likelihood.stderr │ ├── test_3d_log_likelihood.stdout │ ├── test_3d_stream_banded_estimate_1_epoch.stderr │ ├── test_3d_stream_banded_estimate_1_epoch.stdout │ ├── test_3d_stream_estimate_1_epoch.stderr │ ├── test_3d_stream_estimate_1_epoch.stdout │ ├── test_3d_view_fold.stderr │ ├── test_3d_view_fold.stdout │ ├── test_3d_view_fold_npy_from_stdin.stderr │ ├── test_3d_view_fold_npy_from_stdin.stdout │ ├── test_3d_view_normalise.stderr │ ├── test_3d_view_normalise.stdout │ ├── test_3d_view_normalise_npy_output_npy.stderr │ └── test_3d_view_normalise_npy_output_npy.stdout │ └── golden.rs └── winsfs-core ├── Cargo.toml ├── LICENSE-MIT └── src ├── em.rs ├── em ├── adaptors.rs ├── likelihood.rs ├── site.rs ├── standard_em.rs ├── stopping.rs └── window_em.rs ├── io.rs ├── io ├── adaptors.rs ├── shuffle.rs └── shuffle │ ├── header.rs │ ├── reader.rs │ └── writer.rs ├── lib.rs ├── saf.rs ├── saf ├── blocks.rs ├── blocks │ └── spec.rs ├── iter │ ├── mod.rs │ └── sites.rs └── site.rs 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