├── .gitattributes ├── .github └── workflows │ ├── deploy.yml │ └── test.yml ├── .gitignore ├── .pep8speaks.yml ├── .pyup.yml ├── LICENSE ├── MANIFEST.in ├── README.rst ├── allel ├── __init__.py ├── abc.py ├── chunked │ ├── __init__.py │ ├── core.py │ ├── storage_hdf5.py │ ├── storage_zarr.py │ └── util.py ├── compat.py ├── constants.py ├── io │ ├── __init__.py │ ├── fasta.py │ ├── gff.py │ ├── util.py │ ├── vcf_read.py │ └── vcf_write.py ├── model │ ├── __init__.py │ ├── chunked.py │ ├── dask.py │ ├── generic.py │ ├── ndarray.py │ └── util.py ├── opt │ ├── __init__.py │ ├── io_vcf_read.pyx │ ├── model.pyx │ └── stats.pyx ├── plot.py ├── stats │ ├── __init__.py │ ├── admixture.py │ ├── decomposition.py │ ├── distance.py │ ├── diversity.py │ ├── fst.py │ ├── hw.py │ ├── ld.py │ ├── mendel.py │ ├── misc.py │ ├── preprocessing.py │ ├── roh.py │ ├── selection.py │ ├── sf.py │ └── window.py ├── test │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ ├── altlen.vcf │ │ ├── ann.vcf │ │ ├── eff.vcf │ │ ├── empty.vcf │ │ ├── sample.gff │ │ ├── sample.sorted.gff.gz │ │ ├── sample.sorted.gff.gz.tbi │ │ ├── sample.utf8.vcf │ │ ├── sample.vcf │ │ ├── sample.vcf.gz │ │ ├── sample.vcf.gz.tbi │ │ ├── test1.vcf │ │ ├── test14.vcf │ │ ├── test16.vcf │ │ ├── test176.vcf │ │ ├── test32.vcf │ │ ├── test4.vcf │ │ ├── test48a.vcf │ │ ├── test48b.vcf │ │ ├── test54.vcf.gz │ │ ├── test54.vcf.gz.tbi │ │ ├── test63.vcf │ │ └── unsorted.vcf │ ├── io │ │ ├── __init__.py │ │ ├── test_gff_read.py │ │ └── test_vcf_read.py │ ├── model │ │ ├── __init__.py │ │ ├── ndarray │ │ │ ├── __init__.py │ │ │ ├── test_arrays.py │ │ │ ├── test_indexes.py │ │ │ └── test_tables.py │ │ ├── test_api.py │ │ ├── test_chunked.py │ │ └── test_dask.py │ ├── stats │ │ ├── __init__.py │ │ ├── test_mendel.py │ │ ├── test_selection.py │ │ └── test_sf.py │ ├── test_api.py │ ├── test_stats.py │ └── tools.py └── util.py ├── docs ├── Makefile ├── _static │ ├── EXISTS │ └── copybutton.js ├── chunked.rst ├── conf.py ├── index.rst ├── io.rst ├── model.rst ├── model │ ├── chunked.rst │ ├── dask.rst │ ├── ndarray.rst │ └── util.rst ├── release.rst ├── stats.rst ├── stats │ ├── admixture.rst │ ├── decomposition.rst │ ├── distance.rst │ ├── diversity.rst │ ├── fst.rst │ ├── hw.rst │ ├── ld.rst │ ├── mendel.rst │ ├── misc.rst │ ├── preprocessing.rst │ ├── roh.rst │ ├── selection.rst │ ├── sf.rst │ └── window.rst └── util.rst ├── notebooks ├── profiling │ ├── chunked.ipynb │ ├── diversity_divergence.ipynb │ ├── fst.ipynb │ ├── gff3.ipynb │ ├── ihs.ipynb │ ├── ihs_standardization.ipynb │ ├── io_vcf.ipynb │ ├── ld.ipynb │ ├── misc_plotting.ipynb │ ├── model.ipynb │ ├── nsl.ipynb │ ├── pairwise_distance.ipynb │ ├── sfs.ipynb │ ├── spike.vcf.gz │ ├── tables.ipynb │ ├── tajima_d.ipynb │ ├── window_utils.ipynb │ ├── xpehh.ipynb │ └── xpnsl.ipynb ├── repr_html.ipynb └── sandbox │ ├── chunked_repr.ipynb │ ├── dask_bcolz.ipynb │ ├── dask_count_alleles_mask.ipynb │ ├── dask_map_alleles.ipynb │ ├── dask_profiling.ipynb 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