├── .github └── workflows │ ├── ci.yml │ └── docs.yml ├── .gitignore ├── AUTHORS.txt ├── CHANGELOG.md ├── Cargo.lock ├── Cargo.toml ├── LICENSE.md ├── README-rust.md ├── README.md ├── _static ├── _sphinx_javascript_frameworks_compat.js ├── basic.css ├── css │ ├── badge_only.css │ ├── fonts │ │ ├── Roboto-Slab-Bold.woff │ │ ├── Roboto-Slab-Bold.woff2 │ │ ├── Roboto-Slab-Regular.woff │ │ ├── Roboto-Slab-Regular.woff2 │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── lato-bold-italic.woff │ │ ├── lato-bold-italic.woff2 │ │ ├── lato-bold.woff │ │ ├── lato-bold.woff2 │ │ ├── lato-normal-italic.woff │ │ ├── lato-normal-italic.woff2 │ │ ├── lato-normal.woff │ │ └── lato-normal.woff2 │ └── theme.css ├── doctools.js ├── documentation_options.js ├── file.png ├── fonts │ ├── FontAwesome.otf │ ├── Inconsolata-Bold.ttf │ ├── Inconsolata-Regular.ttf │ ├── Inconsolata.ttf │ ├── Lato-Bold.ttf │ ├── Lato-Regular.ttf │ ├── Lato │ │ ├── lato-bold.eot │ │ ├── lato-bold.ttf │ │ ├── lato-bold.woff │ │ ├── lato-bold.woff2 │ │ ├── lato-bolditalic.eot │ │ ├── lato-bolditalic.ttf │ │ ├── lato-bolditalic.woff │ │ ├── lato-bolditalic.woff2 │ │ ├── lato-italic.eot │ │ ├── lato-italic.ttf │ │ ├── lato-italic.woff │ │ ├── lato-italic.woff2 │ │ ├── lato-regular.eot │ │ ├── lato-regular.ttf │ │ ├── lato-regular.woff │ │ └── lato-regular.woff2 │ ├── Roboto-Slab-Bold.woff │ ├── Roboto-Slab-Bold.woff2 │ ├── Roboto-Slab-Light.woff │ ├── Roboto-Slab-Light.woff2 │ ├── Roboto-Slab-Regular.woff │ ├── Roboto-Slab-Regular.woff2 │ ├── Roboto-Slab-Thin.woff │ ├── Roboto-Slab-Thin.woff2 │ ├── RobotoSlab-Bold.ttf │ ├── RobotoSlab-Regular.ttf │ ├── RobotoSlab │ │ ├── roboto-slab-v7-bold.eot │ │ ├── roboto-slab-v7-bold.ttf │ │ ├── roboto-slab-v7-bold.woff │ │ ├── roboto-slab-v7-bold.woff2 │ │ ├── roboto-slab-v7-regular.eot │ │ ├── roboto-slab-v7-regular.ttf │ │ ├── roboto-slab-v7-regular.woff │ │ └── roboto-slab-v7-regular.woff2 │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ ├── fontawesome-webfont.woff │ ├── fontawesome-webfont.woff2 │ ├── lato-bold-italic.woff │ ├── lato-bold-italic.woff2 │ ├── lato-bold.woff │ ├── lato-bold.woff2 │ ├── lato-normal-italic.woff │ ├── lato-normal-italic.woff2 │ ├── lato-normal.woff │ └── lato-normal.woff2 ├── jquery-3.4.1.js ├── jquery-3.5.1.js ├── jquery-3.6.0.js ├── jquery.js ├── js │ ├── badge_only.js │ ├── html5shiv-printshiv.min.js │ ├── html5shiv.min.js │ ├── modernizr.min.js │ └── theme.js ├── language_data.js ├── minus.png ├── plus.png ├── pygments.css ├── searchtools.js ├── sphinx_highlight.js ├── underscore-1.12.0.js ├── underscore-1.13.1.js ├── underscore-1.3.1.js └── underscore.js ├── bed_reader ├── __init__.py ├── _open_bed.py ├── _sample_data.py ├── _to_bed.py └── tests │ ├── __init__.py │ ├── benchmark │ ├── bench2.ipynb │ └── benchmark.py │ ├── data │ ├── 500x400_o640_array.memmap │ ├── badfile.bed │ ├── empty.bed │ ├── plink_sim_10s_100v_10pmiss.bed │ ├── plink_sim_10s_100v_10pmiss.bim │ ├── plink_sim_10s_100v_10pmiss.fam │ ├── small.bad_bim │ ├── small.bed │ ├── small.bim │ ├── small.bim_bad_positions.bim │ ├── small.deb │ ├── small.fam │ ├── small.fam_bad │ ├── small.maf │ ├── small.mib │ ├── small2_array.memmap │ ├── small_array.memmap │ ├── small_no_bim.bed │ ├── small_no_bim.fam │ ├── small_no_fam.bed │ ├── small_no_fam.bim │ ├── small_too_short.bed │ ├── small_too_short.bim │ ├── small_too_short.fam │ ├── smallmode0.bed │ ├── smallmode0.bim │ ├── smallmode0.fam │ ├── smallmodebad.bed │ ├── some_missing.bed │ ├── some_missing.bim │ ├── some_missing.fam │ ├── some_missing.properties.npz │ ├── some_missing.val.npy │ ├── sparse.bed │ ├── sparse.bim │ ├── sparse.fam │ ├── toydata.5chrom.bed │ ├── toydata.5chrom.bim │ └── toydata.5chrom.fam │ ├── registry.txt │ ├── test_file_dot.py │ ├── test_open_bed.py │ ├── test_open_bed_cloud.py │ └── test_opt_dep.py ├── doc ├── Makefile ├── make ├── make.bat └── source │ ├── _static │ └── placeholder.txt │ ├── cloud_urls.rst │ ├── conf.py │ └── index.rst ├── examples ├── cloud.rs └── no_cloud.rs ├── pyproject.toml ├── setpath.bat ├── src ├── bed_cloud.rs ├── lib.rs ├── python_module.rs ├── supplemental_documents │ ├── cloud_urls_etc.md │ └── options_etc.md └── tests.rs ├── tests ├── tests_api.rs └── tests_api_cloud.rs └── useful.md /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fastlmm/bed-reader/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/docs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fastlmm/bed-reader/HEAD/.github/workflows/docs.yml -------------------------------------------------------------------------------- /.gitignore: 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