├── .gitattributes ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── AUTHORS.txt ├── CHANGELOG.md ├── LICENSE.md ├── README.md ├── doc ├── Makefile ├── build │ └── html │ │ ├── .buildinfo │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ └── searchindex.js ├── ipynb │ ├── Derivation normalization.ipynb │ ├── Dist.ipynb │ ├── example1.png │ ├── example2.png │ ├── paper.ipynb │ └── tutorial.ipynb ├── make.bat ├── pynsnptools.html └── source │ ├── Examples.xlsx │ ├── _static │ └── placeholder.txt │ ├── conf.py │ ├── example1.png │ ├── example2.png │ ├── index.rst │ ├── lines.svg │ ├── rust_example1.png │ └── rust_example2.png ├── docs ├── .buildinfo ├── .buildinfo.bak ├── .nojekyll ├── _images │ ├── example1.png │ └── example2.png ├── _sources │ └── index.rst.txt ├── _static │ ├── _sphinx_javascript_frameworks_compat.js │ ├── basic.css │ ├── classic.css │ ├── default.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── jquery-3.5.1.js │ ├── jquery-3.6.0.js │ ├── jquery.js │ ├── language_data.js │ ├── minus.png │ ├── placeholder.txt │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── sidebar.js │ ├── sphinx_highlight.js │ ├── underscore-1.13.1.js │ └── underscore.js ├── genindex.html ├── index.html ├── objects.inv ├── py-modindex.html ├── search.html └── searchindex.js ├── pyproject.toml ├── pysnptools ├── __init__.py ├── distreader │ ├── __init__.py │ ├── _distmergesids.py │ ├── _snp2dist.py │ ├── _subset.py │ ├── bgen.py │ ├── distdata.py │ ├── distgen.py │ ├── disthdf5.py │ ├── distmemmap.py │ ├── distnpz.py │ ├── distreader.py │ ├── test.py │ └── test_bgen2.py ├── examples │ ├── 2500x100.bgen │ ├── 2500x100.bgen.metadata │ ├── bits1.bgen │ ├── bits1.bgen.metadata │ ├── example.bgen │ ├── example.bgen.metadata │ ├── other.sample │ ├── tiny.dist.memmap │ ├── tiny.pst.memmap │ ├── tiny.snp.memmap │ ├── toydata.5chrom.2.fam │ ├── toydata.5chrom.XYMT.bim │ ├── toydata.5chrom.bad.bim │ ├── toydata.5chrom.bed │ ├── toydata.5chrom.bim │ ├── toydata.5chrom.fam │ ├── toydata.bed │ ├── toydata.bim │ ├── toydata.cov │ ├── toydata.dat │ ├── toydata.dist.npz │ ├── toydata.fam │ ├── toydata.fid.phe │ ├── toydata.id.phe │ ├── toydata.iidmajor.dist.hdf5 │ ├── toydata.iidmajor.snp.hdf5 │ ├── toydata.kernel.hdf5 │ ├── toydata.kernel.npz │ ├── toydata.map │ ├── toydata.ped │ ├── toydata.phe │ ├── toydata.shufflePlus.phe │ ├── toydata.sim │ ├── toydata.snpmajor.dist.hdf5 │ ├── toydata.snpmajor.snp.hdf5 │ ├── toydata10.dist.npz │ ├── toydata10.snp.npz │ ├── toydata100.dense.txt │ ├── toydataSkip10.distributedbed │ │ ├── chrom1.piece0of5.bed │ │ ├── chrom1.piece0of5.bim │ │ ├── chrom1.piece0of5.fam │ │ ├── chrom1.piece1of5.bed │ │ ├── chrom1.piece1of5.bim │ │ ├── chrom1.piece1of5.fam │ │ ├── chrom1.piece2of5.bed │ │ ├── chrom1.piece2of5.bim │ │ ├── chrom1.piece2of5.fam │ │ ├── chrom1.piece3of5.bed │ │ ├── chrom1.piece3of5.bim │ │ ├── chrom1.piece3of5.fam │ │ ├── chrom1.piece4of5.bed │ │ ├── chrom1.piece4of5.bim │ │ ├── chrom1.piece4of5.fam │ │ ├── metadata.npz │ │ └── reader_name_list.npz │ └── tutorial.py ├── kernelreader │ ├── __init__.py │ ├── _subset.py │ ├── identity.py │ ├── kerneldata.py │ ├── kernelhdf5.py │ ├── kernelnpz.py │ ├── kernelreader.py │ ├── snpkernel.py │ └── test.py ├── kernelstandardizer │ └── __init__.py ├── pstreader │ ├── __init__.py │ ├── _mergecols.py │ ├── _mergerows.py │ ├── _oneshot.py │ ├── _subset.py │ ├── default.profraw │ ├── pstdata.py │ ├── psthdf5.py │ ├── pstmemmap.py │ ├── pstnpz.py │ ├── pstreader.py │ └── test.py ├── pysnptools.pyproj ├── pysnptools.sln ├── runs │ ├── 2023-05-01_08_52_02_33447698322313224 │ │ └── distributable.p │ └── 2023-05-01_08_52_03_8362610391071055 │ │ └── distributable.p ├── snpreader │ ├── __init__.py │ ├── _dist2snp.py │ ├── _mergeiids.py │ ├── _mergesids.py │ ├── _subset.py │ ├── bed.py │ ├── dat.py │ ├── default.profraw │ ├── dense.py │ ├── distributedbed.py │ ├── pairs.py │ ├── ped.py │ ├── pheno.py │ ├── snpdata.py │ ├── snpgen.py │ ├── snphdf5.py │ ├── snpmemmap.py │ ├── snpnpz.py │ └── snpreader.py ├── standardizer │ ├── __init__.py │ ├── beta.py │ ├── betatrained.py │ ├── bysidcount.py │ ├── bysqrtsidcount.py │ ├── diag_K_to_N.py │ ├── identity.py │ ├── standardizer.py │ ├── unit.py │ └── unittrained.py ├── test.py └── util │ ├── __init__.py │ ├── _example_file.py │ ├── bgen.hashdown.json │ ├── filecache │ ├── __init__.py │ ├── filecache.py │ ├── hashdown.py │ ├── ignore │ │ └── toydata.hashdown.json │ ├── localcache.py │ ├── peertopeer.py │ └── test.py │ ├── generate.py │ ├── intrangeset.py │ ├── mapreduce1 │ ├── __init__.py │ ├── distributable.py │ ├── distributabletest.py │ ├── examples.py │ ├── mapreduce.py │ └── runner │ │ ├── __init__.py │ │ ├── hadoop.py │ │ ├── hadoop2.py │ │ ├── hpc.py │ │ ├── local.py │ │ ├── localinparts.py │ │ ├── localmultiproc.py │ │ ├── localmultithread.py │ │ └── runner.py │ ├── pairs.py │ ├── pheno.py │ ├── pysnptools.hashdown.json │ └── test.py ├── tests ├── 1.0.5b1 ├── 1.12.0 ├── __init__.py ├── datasets │ ├── all_chr.maf0.001.N300.bed │ ├── all_chr.maf0.001.N300.bim │ ├── all_chr.maf0.001.N300.fam │ ├── all_chr.maf0.001.N300.hdf5 │ ├── all_chr.maf0.001.N300.pst.npz │ ├── all_chr.maf0.001.covariates.N300.txt │ ├── distgen.dist.npz │ ├── distributed_bed_test1 │ │ ├── chrom1.piece0of2.bed │ │ ├── chrom1.piece0of2.bim │ │ ├── chrom1.piece0of2.fam │ │ ├── chrom1.piece1of2.bed │ │ ├── chrom1.piece1of2.bim │ │ ├── chrom1.piece1of2.fam │ │ ├── chrom10.piece0of2.bed │ │ ├── chrom10.piece0of2.bim │ │ ├── chrom10.piece0of2.fam │ │ ├── chrom10.piece1of2.bed │ │ ├── chrom10.piece1of2.bim │ │ ├── chrom10.piece1of2.fam │ │ ├── chrom11.piece0of2.bed │ │ ├── chrom11.piece0of2.bim │ │ ├── chrom11.piece0of2.fam │ │ ├── chrom11.piece1of2.bed │ │ ├── chrom11.piece1of2.bim │ │ ├── chrom11.piece1of2.fam │ │ ├── chrom12.piece0of2.bed │ │ ├── chrom12.piece0of2.bim │ │ ├── chrom12.piece0of2.fam │ │ ├── chrom12.piece1of2.bed │ │ ├── chrom12.piece1of2.bim │ │ ├── chrom12.piece1of2.fam │ │ ├── chrom13.piece0of2.bed │ │ ├── chrom13.piece0of2.bim │ │ ├── chrom13.piece0of2.fam │ │ ├── chrom13.piece1of2.bed │ │ ├── chrom13.piece1of2.bim │ │ ├── chrom13.piece1of2.fam │ │ ├── chrom14.piece0of2.bed │ │ ├── chrom14.piece0of2.bim │ │ ├── chrom14.piece0of2.fam │ │ ├── chrom14.piece1of2.bed │ │ ├── chrom14.piece1of2.bim │ │ ├── chrom14.piece1of2.fam │ │ ├── chrom15.piece0of2.bed │ │ ├── chrom15.piece0of2.bim │ │ ├── chrom15.piece0of2.fam │ │ ├── chrom15.piece1of2.bed │ │ ├── chrom15.piece1of2.bim │ │ ├── chrom15.piece1of2.fam │ │ ├── chrom16.piece0of2.bed │ │ ├── chrom16.piece0of2.bim │ │ ├── chrom16.piece0of2.fam │ │ ├── chrom16.piece1of2.bed │ │ ├── chrom16.piece1of2.bim │ │ ├── chrom16.piece1of2.fam │ │ ├── chrom17.piece0of2.bed │ │ ├── chrom17.piece0of2.bim │ │ ├── chrom17.piece0of2.fam │ │ ├── chrom17.piece1of2.bed │ │ ├── chrom17.piece1of2.bim │ │ ├── chrom17.piece1of2.fam │ │ ├── chrom18.piece0of2.bed │ │ ├── chrom18.piece0of2.bim │ │ ├── chrom18.piece0of2.fam │ │ ├── chrom18.piece1of2.bed │ │ ├── chrom18.piece1of2.bim │ │ ├── chrom18.piece1of2.fam │ │ ├── chrom19.piece0of2.bed │ │ ├── chrom19.piece0of2.bim │ │ ├── chrom19.piece0of2.fam │ │ ├── chrom19.piece1of2.bed │ │ ├── chrom19.piece1of2.bim │ │ ├── chrom19.piece1of2.fam │ │ ├── chrom2.piece0of2.bed │ │ ├── chrom2.piece0of2.bim │ │ ├── chrom2.piece0of2.fam │ │ ├── chrom2.piece1of2.bed │ │ ├── chrom2.piece1of2.bim │ │ ├── chrom2.piece1of2.fam │ │ ├── chrom20.piece0of2.bed │ │ ├── chrom20.piece0of2.bim │ │ ├── chrom20.piece0of2.fam │ │ ├── chrom20.piece1of2.bed │ │ ├── chrom20.piece1of2.bim │ │ ├── chrom20.piece1of2.fam │ │ ├── chrom21.piece0of2.bed │ │ ├── chrom21.piece0of2.bim │ │ ├── chrom21.piece0of2.fam │ │ ├── chrom21.piece1of2.bed │ │ ├── chrom21.piece1of2.bim │ │ ├── chrom21.piece1of2.fam │ │ ├── chrom22.piece0of2.bed │ │ ├── chrom22.piece0of2.bim │ │ ├── chrom22.piece0of2.fam │ │ ├── chrom22.piece1of2.bed │ │ ├── chrom22.piece1of2.bim │ │ ├── chrom22.piece1of2.fam │ │ ├── chrom3.piece0of2.bed │ │ ├── chrom3.piece0of2.bim │ │ ├── chrom3.piece0of2.fam │ │ ├── chrom3.piece1of2.bed │ │ ├── chrom3.piece1of2.bim │ │ ├── chrom3.piece1of2.fam │ │ ├── chrom4.piece0of2.bed │ │ ├── chrom4.piece0of2.bim │ │ ├── chrom4.piece0of2.fam │ │ ├── chrom4.piece1of2.bed │ │ ├── chrom4.piece1of2.bim │ │ ├── chrom4.piece1of2.fam │ │ ├── chrom5.piece0of2.bed │ │ ├── chrom5.piece0of2.bim │ │ ├── chrom5.piece0of2.fam │ │ ├── chrom5.piece1of2.bed │ │ ├── chrom5.piece1of2.bim │ │ ├── chrom5.piece1of2.fam │ │ ├── chrom6.piece0of2.bed │ │ ├── chrom6.piece0of2.bim │ │ ├── chrom6.piece0of2.fam │ │ ├── chrom6.piece1of2.bed │ │ ├── chrom6.piece1of2.bim │ │ ├── chrom6.piece1of2.fam │ │ ├── chrom7.piece0of2.bed │ │ ├── chrom7.piece0of2.bim │ │ ├── chrom7.piece0of2.fam │ │ ├── chrom7.piece1of2.bed │ │ ├── chrom7.piece1of2.bim │ │ ├── chrom7.piece1of2.fam │ │ ├── chrom8.piece0of2.bed │ │ ├── chrom8.piece0of2.bim │ │ ├── chrom8.piece0of2.fam │ │ ├── chrom8.piece1of2.bed │ │ ├── chrom8.piece1of2.bim │ │ ├── chrom8.piece1of2.fam │ │ ├── chrom9.piece0of2.bed │ │ ├── chrom9.piece0of2.bim │ │ ├── chrom9.piece0of2.fam │ │ ├── chrom9.piece1of2.bed │ │ ├── chrom9.piece1of2.bim │ │ ├── chrom9.piece1of2.fam │ │ ├── metadata.npz │ │ └── reader_name_list.npz │ ├── distributed_bed_test1_X.bed │ ├── distributed_bed_test1_X.bim │ ├── distributed_bed_test1_X.fam │ ├── generate │ │ ├── gen1.bed │ │ ├── gen1.bim │ │ ├── gen1.fam │ │ ├── gen2.bed │ │ ├── gen2.bim │ │ ├── gen2.fam │ │ ├── gen2b.bed │ │ ├── gen2b.bim │ │ ├── gen2b.fam │ │ ├── gen3.bed │ │ ├── gen3.bim │ │ ├── gen3.fam │ │ ├── gen4.bed │ │ ├── gen4.bim │ │ ├── gen4.fam │ │ ├── gen5.bed │ │ ├── gen5.bim │ │ ├── gen5.fam │ │ ├── gen6.bed │ │ ├── gen6.bim │ │ ├── gen6.fam │ │ ├── gen7.bed │ │ ├── gen7.bim │ │ ├── gen7.fam │ │ ├── gen8a.bed │ │ ├── gen8a.bim │ │ ├── gen8a.fam │ │ ├── gen8b.bed │ │ ├── gen8b.bim │ │ ├── gen8b.fam │ │ 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