From b84fe9f7439026f4c144b4704feb9276c7bceef1 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 17 Sep 2024 15:21:06 +0000 Subject: [PATCH] Update latest documentation --- latest/_sources/changelog.rst.txt | 7 +- .../_sources/examples/gwas_tutorial.ipynb.txt | 18198 +++++++++++----- latest/about.html | 14 +- latest/api.html | 14 +- latest/blog.html | 90 +- latest/blog/2022.html | 90 +- latest/blog/archive.html | 30 +- latest/blog/author.html | 30 +- latest/blog/author/hammer.html | 90 +- latest/blog/category.html | 30 +- latest/blog/category/releases.html | 90 +- latest/blog/drafts.html | 23 +- latest/changelog.html | 76 +- latest/contributing.html | 14 +- latest/examples/gwas_tutorial.html | 1112 +- latest/examples/index.html | 14 +- latest/examples/relatedness_tutorial.html | 129 +- latest/generated/sgkit.Fst.html | 14 +- latest/generated/sgkit.Garud_H.html | 14 +- latest/generated/sgkit.Tajimas_D.html | 14 +- latest/generated/sgkit.Weir_Goudet_beta.html | 14 +- .../sgkit.call_allele_frequencies.html | 14 +- .../sgkit.cohort_allele_frequencies.html | 14 +- .../sgkit.convert_call_to_index.html | 14 +- .../sgkit.convert_probability_to_call.html | 14 +- .../generated/sgkit.count_call_alleles.html | 14 +- .../generated/sgkit.count_cohort_alleles.html | 14 +- .../sgkit.count_variant_alleles.html | 16 +- .../sgkit.count_variant_genotypes.html | 14 +- latest/generated/sgkit.display_genotypes.html | 14 +- latest/generated/sgkit.display_pedigree.html | 14 +- latest/generated/sgkit.divergence.html | 14 +- latest/generated/sgkit.diversity.html | 14 +- .../generated/sgkit.filter_partial_calls.html | 14 +- latest/generated/sgkit.genee.html | 14 +- .../generated/sgkit.genomic_relationship.html | 16 +- .../sgkit.gwas_linear_regression.html | 14 +- .../generated/sgkit.hardy_weinberg_test.html | 14 +- .../sgkit.hybrid_inverse_relationship.html | 16 +- .../generated/sgkit.hybrid_relationship.html | 16 +- latest/generated/sgkit.identity_by_state.html | 16 +- .../sgkit.individual_heterozygosity.html | 14 +- latest/generated/sgkit.infer_call_ploidy.html | 14 +- .../generated/sgkit.infer_sample_ploidy.html | 14 +- .../generated/sgkit.infer_variant_ploidy.html | 14 +- .../sgkit.invert_relationship_matrix.html | 14 +- .../generated/sgkit.io.bgen.bgen_to_zarr.html | 14 +- latest/generated/sgkit.io.bgen.read_bgen.html | 14 +- .../generated/sgkit.io.bgen.rechunk_bgen.html | 14 +- .../sgkit.io.plink.plink_to_zarr.html | 14 +- .../generated/sgkit.io.plink.read_plink.html | 14 +- .../generated/sgkit.io.plink.write_plink.html | 14 +- .../sgkit.io.plink.zarr_to_plink.html | 14 +- .../generated/sgkit.io.vcf.concat_zarrs.html | 14 +- .../sgkit.io.vcf.partition_into_regions.html | 14 +- latest/generated/sgkit.io.vcf.read_vcf.html | 14 +- .../generated/sgkit.io.vcf.vcf_to_zarr.html | 14 +- .../generated/sgkit.io.vcf.vcf_to_zarrs.html | 14 +- latest/generated/sgkit.io.vcf.write_vcf.html | 14 +- .../sgkit.io.vcf.zarr_array_sizes.html | 14 +- .../generated/sgkit.io.vcf.zarr_to_vcf.html | 14 +- latest/generated/sgkit.ld_matrix.html | 14 +- latest/generated/sgkit.ld_prune.html | 14 +- latest/generated/sgkit.load_dataset.html | 14 +- .../sgkit.maximal_independent_set.html | 14 +- .../sgkit.observed_heterozygosity.html | 14 +- latest/generated/sgkit.pairwise_distance.html | 18 +- latest/generated/sgkit.parent_indices.html | 14 +- latest/generated/sgkit.pbs.html | 14 +- latest/generated/sgkit.pc_relate.html | 14 +- .../sgkit.pedigree_contribution.html | 16 +- .../generated/sgkit.pedigree_inbreeding.html | 16 +- .../sgkit.pedigree_inverse_kinship.html | 16 +- latest/generated/sgkit.pedigree_kinship.html | 16 +- latest/generated/sgkit.pedigree_sel.html | 14 +- .../sgkit.read_scikit_allel_vcfzarr.html | 14 +- latest/generated/sgkit.regenie.html | 14 +- latest/generated/sgkit.sample_stats.html | 14 +- latest/generated/sgkit.save_dataset.html | 14 +- latest/generated/sgkit.simulate_genedrop.html | 16 +- .../sgkit.simulate_genotype_call_dataset.html | 14 +- ...gkit.variables.call_allele_count_spec.html | 14 +- ....variables.call_allele_frequency_spec.html | 14 +- ...sgkit.variables.call_dosage_mask_spec.html | 14 +- .../sgkit.variables.call_dosage_spec.html | 16 +- ...bles.call_genotype_complete_mask_spec.html | 14 +- ...variables.call_genotype_complete_spec.html | 14 +- ...kit.variables.call_genotype_fill_spec.html | 14 +- ...riables.call_genotype_index_mask_spec.html | 14 +- ...it.variables.call_genotype_index_spec.html | 14 +- ...kit.variables.call_genotype_mask_spec.html | 14 +- ...t.variables.call_genotype_phased_spec.html | 14 +- ...s.call_genotype_probability_mask_spec.html | 14 +- ...iables.call_genotype_probability_spec.html | 14 +- .../sgkit.variables.call_genotype_spec.html | 14 +- ...it.variables.call_heterozygosity_spec.html | 14 +- .../sgkit.variables.call_ploidy_spec.html | 14 +- ...it.variables.cohort_allele_count_spec.html | 14 +- ...ariables.cohort_allele_frequency_spec.html | 14 +- .../sgkit.variables.covariates_spec.html | 14 +- ...t.variables.interval_contig_name_spec.html | 16 +- .../sgkit.variables.interval_start_spec.html | 14 +- .../sgkit.variables.interval_stop_spec.html | 14 +- ...variables.ld_prune_index_to_drop_spec.html | 14 +- .../sgkit.variables.parent_id_spec.html | 16 +- .../sgkit.variables.parent_spec.html | 14 +- .../sgkit.variables.pc_relate_phi_spec.html | 14 +- ...ariables.regenie_base_prediction_spec.html | 14 +- ...ariables.regenie_loco_prediction_spec.html | 14 +- ...ariables.regenie_meta_prediction_spec.html | 14 +- ...sgkit.variables.sample_call_rate_spec.html | 14 +- .../sgkit.variables.sample_cohort_spec.html | 14 +- .../sgkit.variables.sample_id_spec.html | 16 +- .../sgkit.variables.sample_n_called_spec.html | 14 +- .../sgkit.variables.sample_n_het_spec.html | 14 +- ...sgkit.variables.sample_n_hom_alt_spec.html | 14 +- ...sgkit.variables.sample_n_hom_ref_spec.html | 14 +- ...sgkit.variables.sample_n_non_ref_spec.html | 14 +- ...t.variables.sample_pca_component_spec.html | 14 +- ...ple_pca_explained_variance_ratio_spec.html | 14 +- ...es.sample_pca_explained_variance_spec.html | 14 +- ...kit.variables.sample_pca_loading_spec.html | 14 +- ....variables.sample_pca_projection_spec.html | 14 +- .../sgkit.variables.sample_ploidy_spec.html | 14 +- .../sgkit.variables.stat_Fst_spec.html | 16 +- .../sgkit.variables.stat_Garud_h123_spec.html | 14 +- .../sgkit.variables.stat_Garud_h12_spec.html | 14 +- .../sgkit.variables.stat_Garud_h1_spec.html | 14 +- ...sgkit.variables.stat_Garud_h2_h1_spec.html | 14 +- ...iables.stat_Hamilton_Kerr_lambda_spec.html | 14 +- ...variables.stat_Hamilton_Kerr_tau_spec.html | 14 +- .../sgkit.variables.stat_Tajimas_D_spec.html | 16 +- ....variables.stat_Weir_Goudet_beta_spec.html | 14 +- .../sgkit.variables.stat_divergence_spec.html | 16 +- .../sgkit.variables.stat_diversity_spec.html | 16 +- ...t.variables.stat_genomic_kinship_spec.html | 14 +- ...iables.stat_genomic_relationship_spec.html | 14 +- ...stat_hybrid_inverse_relationship_spec.html | 14 +- ...riables.stat_hybrid_relationship_spec.html | 14 +- ...variables.stat_identity_by_state_spec.html | 14 +- ...iables.stat_inverse_relationship_spec.html | 14 +- ...les.stat_observed_heterozygosity_spec.html | 16 +- .../sgkit.variables.stat_pbs_spec.html | 16 +- ...ables.stat_pedigree_contribution_spec.html | 14 +- ...riables.stat_pedigree_inbreeding_spec.html | 14 +- ...es.stat_pedigree_inverse_kinship_spec.html | 14 +- ...at_pedigree_inverse_relationship_spec.html | 14 +- ....variables.stat_pedigree_kinship_spec.html | 14 +- ...ables.stat_pedigree_relationship_spec.html | 14 +- .../sgkit.variables.traits_spec.html | 14 +- ...t.variables.variant_allele_count_spec.html | 14 +- ...riables.variant_allele_frequency_spec.html | 14 +- .../sgkit.variables.variant_allele_spec.html | 14 +- ...t.variables.variant_allele_total_spec.html | 14 +- ...gkit.variables.variant_call_rate_spec.html | 14 +- .../sgkit.variables.variant_contig_spec.html | 16 +- ...variables.variant_genotype_count_spec.html | 16 +- ...it.variables.variant_hwe_p_value_spec.html | 14 +- .../sgkit.variables.variant_id_spec.html | 16 +- ...it.variables.variant_linreg_beta_spec.html | 14 +- ...variables.variant_linreg_p_value_spec.html | 14 +- ...variables.variant_linreg_t_value_spec.html | 14 +- ...sgkit.variables.variant_n_called_spec.html | 14 +- .../sgkit.variables.variant_n_het_spec.html | 14 +- ...gkit.variables.variant_n_hom_alt_spec.html | 14 +- ...gkit.variables.variant_n_hom_ref_spec.html | 14 +- ...gkit.variables.variant_n_non_ref_spec.html | 14 +- .../sgkit.variables.variant_ploidy_spec.html | 14 +- ...sgkit.variables.variant_position_spec.html | 14 +- .../sgkit.variables.variant_score_spec.html | 14 +- .../sgkit.variables.window_contig_spec.html | 14 +- .../sgkit.variables.window_start_spec.html | 14 +- .../sgkit.variables.window_stop_spec.html | 14 +- latest/generated/sgkit.variant_stats.html | 14 +- latest/generated/sgkit.window_by_genome.html | 14 +- .../generated/sgkit.window_by_interval.html | 14 +- .../generated/sgkit.window_by_position.html | 14 +- latest/generated/sgkit.window_by_variant.html | 14 +- latest/getting_started.html | 14 +- latest/how_do_i.html | 14 +- latest/index.html | 14 +- latest/news.html | 14 +- latest/news/introducing_sgkit.html | 18 +- latest/search.html | 8 +- latest/searchindex.js | 2 +- latest/user_guide.html | 18 +- latest/vcf.html | 14 +- 187 files changed, 14136 insertions(+), 8335 deletions(-) diff --git a/latest/_sources/changelog.rst.txt b/latest/_sources/changelog.rst.txt index 44853cefe..a5263767f 100644 --- a/latest/_sources/changelog.rst.txt +++ b/latest/_sources/changelog.rst.txt @@ -26,8 +26,11 @@ New Features .. Bug fixes .. ~~~~~~~~~ -.. Documentation -.. ~~~~~~~~~~~~~ +Documentation +~~~~~~~~~~~~~ + +- Update GWAS tutorial to use ``vcf2zarr``. + (:user:`tomwhite`, :pr:`1258`, :issue:`1257`) .. _changelog.0.9.0: diff --git a/latest/_sources/examples/gwas_tutorial.ipynb.txt b/latest/_sources/examples/gwas_tutorial.ipynb.txt index ad8fee564..b0d45f25f 100644 --- a/latest/_sources/examples/gwas_tutorial.ipynb.txt +++ b/latest/_sources/examples/gwas_tutorial.ipynb.txt @@ -25,8 +25,7 @@ "metadata": {}, "outputs": [], "source": [ - "import sgkit as sg\n", - "from sgkit.io.vcf import vcf_to_zarr" + "import sgkit as sg" ] }, { @@ -79,8 +78,12 @@ "import requests\n", "\n", "if not Path(\"1kg.vcf.bgz\").exists():\n", - " response = requests.get(\"https://storage.googleapis.com/sgkit-gwas-tutorial/1kg.vcf.bgz\")\n", + " response = requests.get(\"https://storage.googleapis.com/sgkit-data/tutorial/1kg.vcf.bgz\")\n", " with open(\"1kg.vcf.bgz\", \"wb\") as f:\n", + " f.write(response.content)\n", + "if not Path(\"1kg.vcf.bgz.tbi\").exists():\n", + " response = requests.get(\"https://storage.googleapis.com/sgkit-data/tutorial/1kg.vcf.bgz.tbi\")\n", + " with open(\"1kg.vcf.bgz.tbi\", \"wb\") as f:\n", " f.write(response.content)" ] }, @@ -97,27 +100,33 @@ "id": "elementary-college", "metadata": {}, "source": [ - "Next, [convert it to Zarr](https://sgkit-dev.github.io/sgkit/latest/user_guide.html#converting-genetic-data-to-zarr), stored on the local filesystem in a directory called _1kg.zarr_." + "Next, convert the VCF file to Zarr using the `vcf2zarr` command in [bio2zarr](https://sgkit-dev.github.io/bio2zarr/), stored on the local filesystem in a directory called _1kg.vcz_." ] }, { "cell_type": "code", "execution_count": 4, - "id": "composed-injury", + "id": "78effc1d-b45e-4af5-85ae-e0e7a40ca049", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "[W::bcf_hdr_check_sanity] PL should be declared as Number=G\n" + " Scan: 0%| | 0.00/1.00 [00:00 1kg.schema.json # then edit 1kg.schema.json by hand\n", + "vcf2zarr encode --force -s 1kg.schema.json 1kg.icf 1kg.vcz" ] }, { @@ -125,7 +134,11 @@ "id": "plastic-running", "metadata": {}, "source": [ - "We passed a few arguments to the `vcf_to_zarr` conversion function, so it only converts the first alternate allele (`max_alt_alleles=1`), and to load extra VCF fields we are interested in (`GT`, `DP`, `GQ`, and `AD`). Also, `AD` needed defining as having a `Number` definition of `R` (one value for each allele, including the reference), since the dataset we are using defines it as `.` which means \"unknown\".\n", + "We used the `vcf2zarr explode` command to first convert the VCF to an \"intermediate columnar format\" (ICF), then the `vcf2zarr encode` command to convert the ICF to Zarr, which by convention is stored in a directory with a `vcz` extension.\n", + "\n", + "Note that we specified a JSON schema file that was created with the `vcf2zarr mkschema` command (commented out above), then edited to drop some fields that are not needed for this tutorial (such as `FORMAT/PL`). It was also updated to change the `call_AD` field's third dimension to be `alleles`, which was not set by `vcf2zarr` since the dataset we are using defines `FORMAT/AD` as `.` which means \"unknown\", rather than `R`.\n", + "\n", + "For more information about using `vcf2zarr`, see the tutorial in the [bio2zarr documentation](https://sgkit-dev.github.io/bio2zarr/).\n", "\n", "Now the data has been written as Zarr, all downstream operations on will be much faster. Note that sgkit uses an [Xarray](http://xarray.pydata.org/en/stable/) dataset to represent the VCF data, where Hail uses MatrixTable." ] @@ -137,7 +150,7 @@ "metadata": {}, "outputs": [], "source": [ - "ds = sg.load_dataset(\"1kg.zarr\")" + "ds = sg.load_dataset(\"1kg.vcz\")" ] }, { @@ -198,6 +211,7 @@ "}\n", "\n", "html[theme=dark],\n", + "html[data-theme=dark],\n", "body[data-theme=dark],\n", "body.vscode-dark {\n", " --xr-font-color0: rgba(255, 255, 255, 1);\n", @@ -428,6 +442,11 @@ " grid-column: 4;\n", "}\n", "\n", + ".xr-index-preview {\n", + " grid-column: 2 / 5;\n", + " color: var(--xr-font-color2);\n", + "}\n", + "\n", ".xr-var-name,\n", ".xr-var-dims,\n", ".xr-var-dtype,\n", @@ -449,14 +468,16 @@ "}\n", "\n", ".xr-var-attrs,\n", - ".xr-var-data {\n", + ".xr-var-data,\n", + ".xr-index-data {\n", " display: none;\n", " background-color: var(--xr-background-color) !important;\n", " padding-bottom: 5px !important;\n", "}\n", "\n", ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", - ".xr-var-data-in:checked ~ .xr-var-data {\n", + ".xr-var-data-in:checked ~ .xr-var-data,\n", + ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", @@ -466,13 +487,16 @@ "\n", ".xr-var-name span,\n", ".xr-var-data,\n", + ".xr-index-name div,\n", + ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", - ".xr-var-data {\n", + ".xr-var-data,\n", + ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", @@ -510,7 +534,8 @@ "}\n", "\n", ".xr-icon-database,\n", - ".xr-icon-file-text2 {\n", + ".xr-icon-file-text2,\n", + ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", @@ -519,26 +544,26 @@ " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", - "
<xarray.Dataset>\n",
+       "
<xarray.Dataset> Size: 28MB\n",
        "Dimensions:               (variants: 10879, samples: 284, alleles: 2,\n",
        "                           ploidy: 2, contigs: 84, filters: 1)\n",
        "Dimensions without coordinates: variants, samples, alleles, ploidy, contigs,\n",
        "                                filters\n",
        "Data variables: (12/17)\n",
-       "    call_AD               (variants, samples, alleles) int32 dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
-       "    call_DP               (variants, samples) int32 dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
-       "    call_GQ               (variants, samples) int32 dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
-       "    call_genotype         (variants, samples, ploidy) int8 dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
-       "    call_genotype_mask    (variants, samples, ploidy) bool dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
-       "    call_genotype_phased  (variants, samples) bool dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
+       "    call_AD               (variants, samples, alleles) int8 6MB dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
+       "    call_DP               (variants, samples) int8 3MB dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
+       "    call_GQ               (variants, samples) int8 3MB dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
+       "    call_genotype         (variants, samples, ploidy) int8 6MB dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
+       "    call_genotype_mask    (variants, samples, ploidy) bool 6MB dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
+       "    call_genotype_phased  (variants, samples) bool 3MB dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
        "    ...                    ...\n",
-       "    variant_contig        (variants) int8 dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_filter        (variants, filters) bool dask.array<chunksize=(10000, 1), meta=np.ndarray>\n",
-       "    variant_id            (variants) object dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_id_mask       (variants) bool dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_position      (variants) int32 dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_quality       (variants) float32 dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "Attributes: (7)
  • parents
    PandasIndex
    PandasIndex(Index(['SIRE', 'DAM'], dtype='object', name='parents'))

    • Note that the index column of the pedigree dataframe (containing the sample IDs) has been translated to coordinates for the “samples” dimension of the data array. Likewise, the column names have been used as coordinates of the “parents” dimension.

    @@ -1263,7 +1263,7 @@

    Reading pedigree dataReading pedigree dataReading pedigree dataReading pedigree data + dtype='object', name='samples', length=6473))
  • parents
    PandasIndex
    PandasIndex(Index(['SIRE', 'DAM'], dtype='object', name='parents'))
    • @@ -1663,7 +1668,7 @@

    Working with pedigree dataparent_id matrix serves as a robust record of the pedigree structure which preserves the structure of a pedigree if the dataset is subset or reordered. The parent matrix contains integer indices of the parent samples within the dataset allowing for fast numerical calculations. @@ -2080,7 +2090,7 @@

    Pedigree relationshipsPedigree relationshipsPedigree relationshipsPedigree relationships

    Note that the dimensions of the matrices are called samples_0 and samples_1 to avoid using a single dimension twice in an xarray DataArray. Unfortunately, this means that the coordinates of the samples array have not been propagated to the new dimensions. @@ -2527,7 +2542,7 @@

    Pedigree relationshipsPedigree relationshipsPedigree relationshipsPedigree relationships + dtype='object', name='samples_1', length=6473))
  • comment :
    Relationship matrix derived from pedigree structure.

    • We can plot the relationship using matplotlib.

    @@ -3167,7 +3187,7 @@

    Genomic relationshipsGenomic relationshipsGenomic relationshipsGenomic relationships + dtype='object', name='samples', length=3534))

    • Next we create a dataset containing the call_dosage and sample_id variables.

    @@ -3567,7 +3592,7 @@

    Genomic relationshipsGenomic relationshipsGenomic relationshipsGenomic relationships + dtype='object', name='variants', length=1000))

    • @@ -3951,7 +3981,7 @@

    The VanRaden GRM -
    /tmp/ipykernel_2721/892134664.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+
    /tmp/ipykernel_2784/892134664.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims["samples"])
 
    
 
    
@@ -4055,7 +4085,7 @@ 
    A better estimate of ancestral allele frequencies
    -
    /tmp/ipykernel_2721/3477141311.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+
    /tmp/ipykernel_2784/3477141311.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims["samples"])
 
    
 
    
@@ -4127,7 +4157,7 @@ 
    Weir-Goudet GRM
-
    /tmp/ipykernel_2721/70656024.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+
    /tmp/ipykernel_2784/70656024.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims["samples"])
 
    
 
    
@@ -4255,8 +4285,7 @@ 
    References
-  
-  
+   
 
    
 
                 
diff --git a/latest/generated/sgkit.Fst.html b/latest/generated/sgkit.Fst.html
index 323a50b69..5a6e4d7e7 100644
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+++ b/latest/generated/sgkit.Fst.html
@@ -56,13 +56,9 @@
     
     
     
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diff --git a/latest/generated/sgkit.Garud_H.html b/latest/generated/sgkit.Garud_H.html
index 689e67273..443994e85 100644
--- a/latest/generated/sgkit.Garud_H.html
+++ b/latest/generated/sgkit.Garud_H.html
@@ -56,13 +56,9 @@
     
     
     
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@@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.Tajimas_D.html b/latest/generated/sgkit.Tajimas_D.html index 797d432e7..7a99e6e44 100644 --- a/latest/generated/sgkit.Tajimas_D.html +++ b/latest/generated/sgkit.Tajimas_D.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.Weir_Goudet_beta.html b/latest/generated/sgkit.Weir_Goudet_beta.html index a4eb34121..345594dd4 100644 --- a/latest/generated/sgkit.Weir_Goudet_beta.html +++ b/latest/generated/sgkit.Weir_Goudet_beta.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@ diff --git a/latest/generated/sgkit.call_allele_frequencies.html b/latest/generated/sgkit.call_allele_frequencies.html index 8993da7b8..23d5b4485 100644 --- a/latest/generated/sgkit.call_allele_frequencies.html +++ b/latest/generated/sgkit.call_allele_frequencies.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.cohort_allele_frequencies.html b/latest/generated/sgkit.cohort_allele_frequencies.html index d986ef0b8..5139653d8 100644 --- a/latest/generated/sgkit.cohort_allele_frequencies.html +++ b/latest/generated/sgkit.cohort_allele_frequencies.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.convert_call_to_index.html b/latest/generated/sgkit.convert_call_to_index.html index 9dbeefc5a..f7d920eb4 100644 --- a/latest/generated/sgkit.convert_call_to_index.html +++ b/latest/generated/sgkit.convert_call_to_index.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.convert_probability_to_call.html b/latest/generated/sgkit.convert_probability_to_call.html index be9db18fa..cee2f286a 100644 --- a/latest/generated/sgkit.convert_probability_to_call.html +++ b/latest/generated/sgkit.convert_probability_to_call.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.count_call_alleles.html b/latest/generated/sgkit.count_call_alleles.html index b534a8a2b..88ff74cf0 100644 --- a/latest/generated/sgkit.count_call_alleles.html +++ b/latest/generated/sgkit.count_call_alleles.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.count_cohort_alleles.html b/latest/generated/sgkit.count_cohort_alleles.html index 8952bcafb..4c204c0c5 100644 --- a/latest/generated/sgkit.count_cohort_alleles.html +++ b/latest/generated/sgkit.count_cohort_alleles.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.count_variant_alleles.html b/latest/generated/sgkit.count_variant_alleles.html index 259a66d5e..412979884 100644 --- a/latest/generated/sgkit.count_variant_alleles.html +++ b/latest/generated/sgkit.count_variant_alleles.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.count_variant_alleles#

    @@ -765,7 +760,7 @@

    sgkit.count_variant_allelesds, it will be computed using count_call_alleles().

    -
    using Literal['call_allele_count', 'call_genotype'] (default: 'call_allele_count')

    specify the variable used to calculate allele counts from. +

    using {‘call_allele_count’, ‘call_genotype’}Literal['call_allele_count', 'call_genotype'] (default: 'call_allele_count')

    specify the variable used to calculate allele counts from. If 'call_allele_count' (the default), the result will be calculated from the call_allele_count variable. If 'call_genotype', the result will be calculated from @@ -819,8 +814,7 @@

    sgkit.count_variant_alleles - - +

    diff --git a/latest/generated/sgkit.count_variant_genotypes.html b/latest/generated/sgkit.count_variant_genotypes.html index fbe62abc1..6cc7a1a9b 100644 --- a/latest/generated/sgkit.count_variant_genotypes.html +++ b/latest/generated/sgkit.count_variant_genotypes.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.display_genotypes.html b/latest/generated/sgkit.display_genotypes.html index cdf76cc11..87201e1ba 100644 --- a/latest/generated/sgkit.display_genotypes.html +++ b/latest/generated/sgkit.display_genotypes.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.display_pedigree.html b/latest/generated/sgkit.display_pedigree.html index 783c73ca9..5b3e0b818 100644 --- a/latest/generated/sgkit.display_pedigree.html +++ b/latest/generated/sgkit.display_pedigree.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.divergence.html b/latest/generated/sgkit.divergence.html index 099f25f90..b0ccc45c7 100644 --- a/latest/generated/sgkit.divergence.html +++ b/latest/generated/sgkit.divergence.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.diversity.html b/latest/generated/sgkit.diversity.html index e43537f3d..9493d9ca6 100644 --- a/latest/generated/sgkit.diversity.html +++ b/latest/generated/sgkit.diversity.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.filter_partial_calls.html b/latest/generated/sgkit.filter_partial_calls.html index 3207a8f63..2b3bfb967 100644 --- a/latest/generated/sgkit.filter_partial_calls.html +++ b/latest/generated/sgkit.filter_partial_calls.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.genee.html b/latest/generated/sgkit.genee.html index 1226e2a31..2276999a1 100644 --- a/latest/generated/sgkit.genee.html +++ b/latest/generated/sgkit.genee.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.genomic_relationship.html b/latest/generated/sgkit.genomic_relationship.html index e4df6c8f3..c02596016 100644 --- a/latest/generated/sgkit.genomic_relationship.html +++ b/latest/generated/sgkit.genomic_relationship.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.genomic_relationship#

    @@ -766,7 +761,7 @@

    sgkit.genomic_relationshipHashable (default: 'call_dosage')

    Input variable name holding call_dosage as defined by sgkit.variables.call_dosage_spec.

    -
    estimator Literal['VanRaden', 'Endelman-Jannink'] | NoneOptional[Literal['VanRaden', 'Endelman-Jannink']] (default: None)

    Specifies the relatedness estimator to use. Must be one of +

    estimator {‘VanRaden’, ‘Endelman-Jannink’} | NoneOptional[Literal['VanRaden', 'Endelman-Jannink']] (default: None)

    Specifies the relatedness estimator to use. Must be one of 'VanRaden' (the default) or 'Endelman-Jannink'.

    ancestral_frequency Hashable | NoneOptional[Hashable] (default: None)

    Frequency of variant alleles corresponding to call_dosage within @@ -946,8 +941,7 @@

    sgkit.genomic_relationship - - +

    diff --git a/latest/generated/sgkit.gwas_linear_regression.html b/latest/generated/sgkit.gwas_linear_regression.html index 3fa446e30..619b0e44d 100644 --- a/latest/generated/sgkit.gwas_linear_regression.html +++ b/latest/generated/sgkit.gwas_linear_regression.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.hardy_weinberg_test.html b/latest/generated/sgkit.hardy_weinberg_test.html index ea33c1cf7..f3eee2b1e 100644 --- a/latest/generated/sgkit.hardy_weinberg_test.html +++ b/latest/generated/sgkit.hardy_weinberg_test.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.hybrid_inverse_relationship.html b/latest/generated/sgkit.hybrid_inverse_relationship.html index e55d65a08..0e331931f 100644 --- a/latest/generated/sgkit.hybrid_inverse_relationship.html +++ b/latest/generated/sgkit.hybrid_inverse_relationship.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@
    - -
    +

    sgkit.hybrid_inverse_relationship#

    @@ -775,7 +770,7 @@

    sgkit.hybrid_inverse_relationshipLiteral['Martini'] | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option +

    estimator {‘Martini’} | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option is "Martini" following Martini et al 2018 [1] which expands on the estimators of Legarra et al 2009 [2] and Aguiler et al 2010 [3].

    @@ -900,8 +895,7 @@

    sgkit.hybrid_inverse_relationship - - +

    diff --git a/latest/generated/sgkit.hybrid_relationship.html b/latest/generated/sgkit.hybrid_relationship.html index 61ac2b45d..4b24e0e3a 100644 --- a/latest/generated/sgkit.hybrid_relationship.html +++ b/latest/generated/sgkit.hybrid_relationship.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@
    - -
    +

    sgkit.hybrid_relationship#

    @@ -778,7 +773,7 @@

    sgkit.hybrid_relationshipLiteral['Martini'] | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option +

    estimator {‘Martini’} | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option is "Martini" following Martini et al 2018 [1] which expands on the estimators of Legarra et al 2009 [2] and Aguiler et al 2010 [3].

    @@ -884,8 +879,7 @@

    sgkit.hybrid_relationship - - +

    diff --git a/latest/generated/sgkit.identity_by_state.html b/latest/generated/sgkit.identity_by_state.html index 1a9f5f755..6f79de54e 100644 --- a/latest/generated/sgkit.identity_by_state.html +++ b/latest/generated/sgkit.identity_by_state.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.identity_by_state#

    @@ -770,7 +765,7 @@

    sgkit.identity_by_stateds, it will be computed using call_allele_frequencies().

    -
    method Literal['frequencies', 'matching'] (default: 'frequencies')

    The method used for IBS estimation. Defaults to “frequencies” +

    method {‘frequencies’, ‘matching’}Literal['frequencies', 'matching'] (default: 'frequencies')

    The method used for IBS estimation. Defaults to “frequencies” which calculates IBS probabilities by matrix multiplication of call allele frequencies which is more efficient when the alleles dimension is small. @@ -818,8 +813,7 @@

    sgkit.identity_by_state
    - - +

    diff --git a/latest/generated/sgkit.individual_heterozygosity.html b/latest/generated/sgkit.individual_heterozygosity.html index 66f0dafe2..58f4c5ac0 100644 --- a/latest/generated/sgkit.individual_heterozygosity.html +++ b/latest/generated/sgkit.individual_heterozygosity.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.infer_call_ploidy.html b/latest/generated/sgkit.infer_call_ploidy.html index 96c427992..a0d3eb2c8 100644 --- a/latest/generated/sgkit.infer_call_ploidy.html +++ b/latest/generated/sgkit.infer_call_ploidy.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.infer_sample_ploidy.html b/latest/generated/sgkit.infer_sample_ploidy.html index c8fdb7e21..0cf1d1f9c 100644 --- a/latest/generated/sgkit.infer_sample_ploidy.html +++ b/latest/generated/sgkit.infer_sample_ploidy.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.infer_variant_ploidy.html b/latest/generated/sgkit.infer_variant_ploidy.html index 57d0aecfa..01b23a980 100644 --- a/latest/generated/sgkit.infer_variant_ploidy.html +++ b/latest/generated/sgkit.infer_variant_ploidy.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.invert_relationship_matrix.html b/latest/generated/sgkit.invert_relationship_matrix.html index 4f3579ce8..af39f7d13 100644 --- a/latest/generated/sgkit.invert_relationship_matrix.html +++ b/latest/generated/sgkit.invert_relationship_matrix.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.bgen.bgen_to_zarr.html b/latest/generated/sgkit.io.bgen.bgen_to_zarr.html index 1e3f8eaee..d086397ab 100644 --- a/latest/generated/sgkit.io.bgen.bgen_to_zarr.html +++ b/latest/generated/sgkit.io.bgen.bgen_to_zarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.bgen.read_bgen.html b/latest/generated/sgkit.io.bgen.read_bgen.html index a5c917c99..f192c3745 100644 --- a/latest/generated/sgkit.io.bgen.read_bgen.html +++ b/latest/generated/sgkit.io.bgen.read_bgen.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.bgen.rechunk_bgen.html b/latest/generated/sgkit.io.bgen.rechunk_bgen.html index 12cf1c78e..6e7f7b267 100644 --- a/latest/generated/sgkit.io.bgen.rechunk_bgen.html +++ b/latest/generated/sgkit.io.bgen.rechunk_bgen.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.plink_to_zarr.html b/latest/generated/sgkit.io.plink.plink_to_zarr.html index 6f8d9697a..5f1e097fa 100644 --- a/latest/generated/sgkit.io.plink.plink_to_zarr.html +++ b/latest/generated/sgkit.io.plink.plink_to_zarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.read_plink.html b/latest/generated/sgkit.io.plink.read_plink.html index 3ae50fa9b..197d77090 100644 --- a/latest/generated/sgkit.io.plink.read_plink.html +++ b/latest/generated/sgkit.io.plink.read_plink.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.write_plink.html b/latest/generated/sgkit.io.plink.write_plink.html index 51ae1dd7c..fc9f72e8d 100644 --- a/latest/generated/sgkit.io.plink.write_plink.html +++ b/latest/generated/sgkit.io.plink.write_plink.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.zarr_to_plink.html b/latest/generated/sgkit.io.plink.zarr_to_plink.html index beaca87c9..6bf6eae2d 100644 --- a/latest/generated/sgkit.io.plink.zarr_to_plink.html +++ b/latest/generated/sgkit.io.plink.zarr_to_plink.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.concat_zarrs.html b/latest/generated/sgkit.io.vcf.concat_zarrs.html index 5004eb90a..43c0e5caa 100644 --- a/latest/generated/sgkit.io.vcf.concat_zarrs.html +++ b/latest/generated/sgkit.io.vcf.concat_zarrs.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.partition_into_regions.html b/latest/generated/sgkit.io.vcf.partition_into_regions.html index da03d6fe2..7829f0778 100644 --- a/latest/generated/sgkit.io.vcf.partition_into_regions.html +++ b/latest/generated/sgkit.io.vcf.partition_into_regions.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.read_vcf.html b/latest/generated/sgkit.io.vcf.read_vcf.html index 24477ed72..8cb0d94d6 100644 --- a/latest/generated/sgkit.io.vcf.read_vcf.html +++ b/latest/generated/sgkit.io.vcf.read_vcf.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.vcf_to_zarr.html b/latest/generated/sgkit.io.vcf.vcf_to_zarr.html index 2370dfe9e..5fa2192f7 100644 --- a/latest/generated/sgkit.io.vcf.vcf_to_zarr.html +++ b/latest/generated/sgkit.io.vcf.vcf_to_zarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html b/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html index 72baf1772..216e8c75b 100644 --- a/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html +++ b/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.write_vcf.html b/latest/generated/sgkit.io.vcf.write_vcf.html index 68f62feb0..d74b32b9a 100644 --- a/latest/generated/sgkit.io.vcf.write_vcf.html +++ b/latest/generated/sgkit.io.vcf.write_vcf.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.zarr_array_sizes.html b/latest/generated/sgkit.io.vcf.zarr_array_sizes.html index 8fbd1b11c..58445713f 100644 --- a/latest/generated/sgkit.io.vcf.zarr_array_sizes.html +++ b/latest/generated/sgkit.io.vcf.zarr_array_sizes.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.zarr_to_vcf.html b/latest/generated/sgkit.io.vcf.zarr_to_vcf.html index ef4bb749e..9518723c4 100644 --- a/latest/generated/sgkit.io.vcf.zarr_to_vcf.html +++ b/latest/generated/sgkit.io.vcf.zarr_to_vcf.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.ld_matrix.html b/latest/generated/sgkit.ld_matrix.html index 14f96c745..e013fbccb 100644 --- a/latest/generated/sgkit.ld_matrix.html +++ b/latest/generated/sgkit.ld_matrix.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.ld_prune.html b/latest/generated/sgkit.ld_prune.html index 2a85a604d..eac23f876 100644 --- a/latest/generated/sgkit.ld_prune.html +++ b/latest/generated/sgkit.ld_prune.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.load_dataset.html b/latest/generated/sgkit.load_dataset.html index fb3fca649..b8de7fdee 100644 --- a/latest/generated/sgkit.load_dataset.html +++ b/latest/generated/sgkit.load_dataset.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.maximal_independent_set.html b/latest/generated/sgkit.maximal_independent_set.html index dd17988f1..4ddb5d299 100644 --- a/latest/generated/sgkit.maximal_independent_set.html +++ b/latest/generated/sgkit.maximal_independent_set.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.observed_heterozygosity.html b/latest/generated/sgkit.observed_heterozygosity.html index c7b674799..de1f0a1a8 100644 --- a/latest/generated/sgkit.observed_heterozygosity.html +++ b/latest/generated/sgkit.observed_heterozygosity.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pairwise_distance.html b/latest/generated/sgkit.pairwise_distance.html index 261a859a6..1b8cf889f 100644 --- a/latest/generated/sgkit.pairwise_distance.html +++ b/latest/generated/sgkit.pairwise_distance.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pairwise_distance#

    @@ -781,7 +776,7 @@

    sgkit.pairwise_distance -
    metric Literal['euclidean', 'correlation'] (default: 'euclidean')

    The distance metric to use. The distance function can be +

    metric {‘euclidean’, ‘correlation’}Literal['euclidean', 'correlation'] (default: 'euclidean')

    The distance metric to use. The distance function can be ‘euclidean’ or ‘correlation’.

    split_every int | NoneOptional[int] (default: None)

    Determines the depth of the recursive aggregation in the reduction @@ -791,7 +786,7 @@

    sgkit.pairwise_distance

    -
    device Literal['cpu', 'gpu'] (default: 'cpu')

    The architecture to run the calculation on, either of “cpu” or “gpu”

    +
    device {‘cpu’, ‘gpu’}Literal['cpu', 'gpu'] (default: 'cpu')

    The architecture to run the calculation on, either of “cpu” or “gpu”

    @@ -838,8 +833,7 @@

    sgkit.pairwise_distance
    - - +

    diff --git a/latest/generated/sgkit.parent_indices.html b/latest/generated/sgkit.parent_indices.html index 82cc66ecf..0aeda1fc3 100644 --- a/latest/generated/sgkit.parent_indices.html +++ b/latest/generated/sgkit.parent_indices.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pbs.html b/latest/generated/sgkit.pbs.html index 71a761c6a..62ab3379d 100644 --- a/latest/generated/sgkit.pbs.html +++ b/latest/generated/sgkit.pbs.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pc_relate.html b/latest/generated/sgkit.pc_relate.html index c9871a224..f40629432 100644 --- a/latest/generated/sgkit.pc_relate.html +++ b/latest/generated/sgkit.pc_relate.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pedigree_contribution.html b/latest/generated/sgkit.pedigree_contribution.html index 1e4774143..37b495b74 100644 --- a/latest/generated/sgkit.pedigree_contribution.html +++ b/latest/generated/sgkit.pedigree_contribution.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pedigree_contribution#

    @@ -756,7 +751,7 @@

    sgkit.pedigree_contribution
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['even', 'variable'] (default: 'even')

    The method used for estimating genomic contributions. +

    method {‘even’, ‘variable’}Literal['even', 'variable'] (default: 'even')

    The method used for estimating genomic contributions. The ‘even’ method assumes that all samples are of a single, even ploidy (e.g., diploid) and have even contributions from each parent. The ‘variable’ method allows for un-even @@ -831,8 +826,7 @@

    sgkit.pedigree_contribution - - +

    diff --git a/latest/generated/sgkit.pedigree_inbreeding.html b/latest/generated/sgkit.pedigree_inbreeding.html index 4acf32d40..f312e0438 100644 --- a/latest/generated/sgkit.pedigree_inbreeding.html +++ b/latest/generated/sgkit.pedigree_inbreeding.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@
    - -
    +

    sgkit.pedigree_inbreeding#

    @@ -757,7 +752,7 @@

    sgkit.pedigree_inbreeding
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for inbreeding estimation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’}Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for inbreeding estimation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -915,8 +910,7 @@

    sgkit.pedigree_inbreeding - - +

    diff --git a/latest/generated/sgkit.pedigree_inverse_kinship.html b/latest/generated/sgkit.pedigree_inverse_kinship.html index 89cf61c4d..ce274f679 100644 --- a/latest/generated/sgkit.pedigree_inverse_kinship.html +++ b/latest/generated/sgkit.pedigree_inverse_kinship.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pedigree_inverse_kinship#

    @@ -757,7 +752,7 @@

    sgkit.pedigree_inverse_kinship
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’}Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -928,8 +923,7 @@

    sgkit.pedigree_inverse_kinship - - +

    diff --git a/latest/generated/sgkit.pedigree_kinship.html b/latest/generated/sgkit.pedigree_kinship.html index 24fe3a66a..876715c3b 100644 --- a/latest/generated/sgkit.pedigree_kinship.html +++ b/latest/generated/sgkit.pedigree_kinship.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pedigree_kinship#

    @@ -757,7 +752,7 @@

    sgkit.pedigree_kinship
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’}Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -996,8 +991,7 @@

    sgkit.pedigree_kinship
    - - +

    diff --git a/latest/generated/sgkit.pedigree_sel.html b/latest/generated/sgkit.pedigree_sel.html index a355f3ab8..62f15ce40 100644 --- a/latest/generated/sgkit.pedigree_sel.html +++ b/latest/generated/sgkit.pedigree_sel.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.read_scikit_allel_vcfzarr.html b/latest/generated/sgkit.read_scikit_allel_vcfzarr.html index b93029e03..0911b8037 100644 --- a/latest/generated/sgkit.read_scikit_allel_vcfzarr.html +++ b/latest/generated/sgkit.read_scikit_allel_vcfzarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.regenie.html b/latest/generated/sgkit.regenie.html index 3ea2f144f..70fc0b4d5 100644 --- a/latest/generated/sgkit.regenie.html +++ b/latest/generated/sgkit.regenie.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.sample_stats.html b/latest/generated/sgkit.sample_stats.html index fa95cefca..2f140eac7 100644 --- a/latest/generated/sgkit.sample_stats.html +++ b/latest/generated/sgkit.sample_stats.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.save_dataset.html b/latest/generated/sgkit.save_dataset.html index ddc50fcbd..09843fbc3 100644 --- a/latest/generated/sgkit.save_dataset.html +++ b/latest/generated/sgkit.save_dataset.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.simulate_genedrop.html b/latest/generated/sgkit.simulate_genedrop.html index 312b4506c..f4c99b83c 100644 --- a/latest/generated/sgkit.simulate_genedrop.html +++ b/latest/generated/sgkit.simulate_genedrop.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.simulate_genedrop#

    @@ -758,7 +753,7 @@

    sgkit.simulate_genedrop
    ds Dataset

    Dataset containing genotype calls and pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] | NoneOptional[Literal['diploid', 'Hamilton-Kerr']] (default: 'diploid')

    The method used for gene-drop simulation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’} | NoneOptional[Literal['diploid', 'Hamilton-Kerr']] (default: 'diploid')

    The method used for gene-drop simulation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -893,8 +888,7 @@

    sgkit.simulate_genedrop
    - - +

    diff --git a/latest/generated/sgkit.simulate_genotype_call_dataset.html b/latest/generated/sgkit.simulate_genotype_call_dataset.html index 15b5bbf9d..717b14489 100644 --- a/latest/generated/sgkit.simulate_genotype_call_dataset.html +++ b/latest/generated/sgkit.simulate_genotype_call_dataset.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_allele_count_spec.html b/latest/generated/sgkit.variables.call_allele_count_spec.html index a8f2aafd9..79ab096e6 100644 --- a/latest/generated/sgkit.variables.call_allele_count_spec.html +++ b/latest/generated/sgkit.variables.call_allele_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_allele_frequency_spec.html b/latest/generated/sgkit.variables.call_allele_frequency_spec.html index b80c2d25d..650e8c025 100644 --- a/latest/generated/sgkit.variables.call_allele_frequency_spec.html +++ b/latest/generated/sgkit.variables.call_allele_frequency_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_dosage_mask_spec.html b/latest/generated/sgkit.variables.call_dosage_mask_spec.html index b2a3c7306..308c9ac6d 100644 --- a/latest/generated/sgkit.variables.call_dosage_mask_spec.html +++ b/latest/generated/sgkit.variables.call_dosage_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_dosage_spec.html b/latest/generated/sgkit.variables.call_dosage_spec.html index 6146bde64..870c7cdfa 100644 --- a/latest/generated/sgkit.variables.call_dosage_spec.html +++ b/latest/generated/sgkit.variables.call_dosage_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.call_dosage_spec#

    -sgkit.variables.call_dosage_spec = ArrayLikeSpec(default_name='call_dosage', __doc__='\nDosages, encoded as floats, with NaN indicating a missing value.\nDosages can represent one of several possible quantities, e.g.:\n- Alternate allele counts\n- Recessive or dominant allele encodings\n- True dosages as computed from imputed or probabilistic variant calls\n- Any other custom encoding in a user-defined variable\n', kind={'f', 'i', 'u'}, ndim=2, dims=('variants', 'samples'))#
    +sgkit.variables.call_dosage_spec = ArrayLikeSpec(default_name='call_dosage', __doc__='\nDosages, encoded as floats, with NaN indicating a missing value.\nDosages can represent one of several possible quantities, e.g.:\n- Alternate allele counts\n- Recessive or dominant allele encodings\n- True dosages as computed from imputed or probabilistic variant calls\n- Any other custom encoding in a user-defined variable\n', kind={'u', 'f', 'i'}, ndim=2, dims=('variants', 'samples'))#

    Dosages, encoded as floats, with NaN indicating a missing value. Dosages can represent one of several possible quantities, e.g.: - Alternate allele counts @@ -760,8 +755,7 @@

    sgkit.variables.call_dosage_spec - - +

    diff --git a/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html index b5e17e55d..309f4bdc2 100644 --- a/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_complete_spec.html b/latest/generated/sgkit.variables.call_genotype_complete_spec.html index a57c2e7d4..15b46c265 100644 --- a/latest/generated/sgkit.variables.call_genotype_complete_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_complete_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_fill_spec.html b/latest/generated/sgkit.variables.call_genotype_fill_spec.html index f23415c56..94ebbc43f 100644 --- a/latest/generated/sgkit.variables.call_genotype_fill_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_fill_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html index 571a94677..aa1b1fb6d 100644 --- a/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_index_spec.html b/latest/generated/sgkit.variables.call_genotype_index_spec.html index b743c27a4..d8b350a93 100644 --- a/latest/generated/sgkit.variables.call_genotype_index_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_index_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_mask_spec.html index 5f833c13c..cb0ea4954 100644 --- a/latest/generated/sgkit.variables.call_genotype_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_phased_spec.html b/latest/generated/sgkit.variables.call_genotype_phased_spec.html index db6c919bb..742c8caba 100644 --- a/latest/generated/sgkit.variables.call_genotype_phased_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_phased_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html index a031ab07b..63f7078c9 100644 --- a/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_probability_spec.html b/latest/generated/sgkit.variables.call_genotype_probability_spec.html index 1ab9a4e5f..e7970b9b6 100644 --- a/latest/generated/sgkit.variables.call_genotype_probability_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_probability_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_spec.html b/latest/generated/sgkit.variables.call_genotype_spec.html index 3b3d75ba8..d8fa063b1 100644 --- a/latest/generated/sgkit.variables.call_genotype_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_heterozygosity_spec.html b/latest/generated/sgkit.variables.call_heterozygosity_spec.html index 55c75206a..bdc70106b 100644 --- a/latest/generated/sgkit.variables.call_heterozygosity_spec.html +++ b/latest/generated/sgkit.variables.call_heterozygosity_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_ploidy_spec.html b/latest/generated/sgkit.variables.call_ploidy_spec.html index 9817b7cf3..e0898dbea 100644 --- a/latest/generated/sgkit.variables.call_ploidy_spec.html +++ b/latest/generated/sgkit.variables.call_ploidy_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.cohort_allele_count_spec.html b/latest/generated/sgkit.variables.cohort_allele_count_spec.html index 7c8895dac..719f07b85 100644 --- a/latest/generated/sgkit.variables.cohort_allele_count_spec.html +++ b/latest/generated/sgkit.variables.cohort_allele_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html b/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html index c57f54971..eb22e3369 100644 --- a/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html +++ b/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.covariates_spec.html b/latest/generated/sgkit.variables.covariates_spec.html index 0c8fbf3d2..d42347e57 100644 --- a/latest/generated/sgkit.variables.covariates_spec.html +++ b/latest/generated/sgkit.variables.covariates_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.interval_contig_name_spec.html b/latest/generated/sgkit.variables.interval_contig_name_spec.html index 621533931..e7274f65b 100644 --- a/latest/generated/sgkit.variables.interval_contig_name_spec.html +++ b/latest/generated/sgkit.variables.interval_contig_name_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.interval_contig_name_spec#

    -sgkit.variables.interval_contig_name_spec = ArrayLikeSpec(default_name='interval_contig_name', __doc__='Interval contig name. Must match a contig defined in the ``contigs`` attribute.', kind={'U', 'S', 'O'}, ndim=1, dims=None)#
    +sgkit.variables.interval_contig_name_spec = ArrayLikeSpec(default_name='interval_contig_name', __doc__='Interval contig name. Must match a contig defined in the ``contigs`` attribute.', kind={'S', 'U', 'O'}, ndim=1, dims=None)#

    Interval contig name. Must match a contig defined in the contigs attribute.

    - - +
    diff --git a/latest/generated/sgkit.variables.interval_start_spec.html b/latest/generated/sgkit.variables.interval_start_spec.html index aa8775497..51751067d 100644 --- a/latest/generated/sgkit.variables.interval_start_spec.html +++ b/latest/generated/sgkit.variables.interval_start_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.interval_start_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.interval_start_spec - - +

    diff --git a/latest/generated/sgkit.variables.interval_stop_spec.html b/latest/generated/sgkit.variables.interval_stop_spec.html index ae1f27e35..ff72547a2 100644 --- a/latest/generated/sgkit.variables.interval_stop_spec.html +++ b/latest/generated/sgkit.variables.interval_stop_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html b/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html index 86c6b9b68..f9526f0a9 100644 --- a/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html +++ b/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.parent_id_spec.html b/latest/generated/sgkit.variables.parent_id_spec.html index 292cd9dcd..cf255f734 100644 --- a/latest/generated/sgkit.variables.parent_id_spec.html +++ b/latest/generated/sgkit.variables.parent_id_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.parent_id_spec#

    -sgkit.variables.parent_id_spec = ArrayLikeSpec(default_name='parent_id', __doc__='\nUnique identifiers of parent samples matching those in\n:data:`sgkit.variables.sample_id_spec`.\n', kind={'U', 'S', 'O'}, ndim=2, dims=('samples', 'parents'))#
    +sgkit.variables.parent_id_spec = ArrayLikeSpec(default_name='parent_id', __doc__='\nUnique identifiers of parent samples matching those in\n:data:`sgkit.variables.sample_id_spec`.\n', kind={'S', 'U', 'O'}, ndim=2, dims=('samples', 'parents'))#

    Unique identifiers of parent samples matching those in sgkit.variables.sample_id_spec.

    @@ -756,8 +751,7 @@

    sgkit.variables.parent_id_spec - - +

    diff --git a/latest/generated/sgkit.variables.parent_spec.html b/latest/generated/sgkit.variables.parent_spec.html index 414969887..8c1c1e7d1 100644 --- a/latest/generated/sgkit.variables.parent_spec.html +++ b/latest/generated/sgkit.variables.parent_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.pc_relate_phi_spec.html b/latest/generated/sgkit.variables.pc_relate_phi_spec.html index 0649b17df..ba7d497da 100644 --- a/latest/generated/sgkit.variables.pc_relate_phi_spec.html +++ b/latest/generated/sgkit.variables.pc_relate_phi_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.regenie_base_prediction_spec.html b/latest/generated/sgkit.variables.regenie_base_prediction_spec.html index 89e35d48b..a4f4754e0 100644 --- a/latest/generated/sgkit.variables.regenie_base_prediction_spec.html +++ b/latest/generated/sgkit.variables.regenie_base_prediction_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html b/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html index 4a843eb8c..f59cc6264 100644 --- a/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html +++ b/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html b/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html index cd3011023..0017b6322 100644 --- a/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html +++ b/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_call_rate_spec.html b/latest/generated/sgkit.variables.sample_call_rate_spec.html index 833009d73..810a476b0 100644 --- a/latest/generated/sgkit.variables.sample_call_rate_spec.html +++ b/latest/generated/sgkit.variables.sample_call_rate_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_cohort_spec.html b/latest/generated/sgkit.variables.sample_cohort_spec.html index 67b917b09..e0d84fe20 100644 --- a/latest/generated/sgkit.variables.sample_cohort_spec.html +++ b/latest/generated/sgkit.variables.sample_cohort_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_id_spec.html b/latest/generated/sgkit.variables.sample_id_spec.html index 6bc6ff4d0..84f6a555f 100644 --- a/latest/generated/sgkit.variables.sample_id_spec.html +++ b/latest/generated/sgkit.variables.sample_id_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.sample_id_spec#

    -sgkit.variables.sample_id_spec = ArrayLikeSpec(default_name='sample_id', __doc__='The unique identifier of the sample.', kind={'U', 'S', 'O'}, ndim=1, dims=('samples',))#
    +sgkit.variables.sample_id_spec = ArrayLikeSpec(default_name='sample_id', __doc__='The unique identifier of the sample.', kind={'S', 'U', 'O'}, ndim=1, dims=('samples',))#

    The unique identifier of the sample.

    - - +
    diff --git a/latest/generated/sgkit.variables.sample_n_called_spec.html b/latest/generated/sgkit.variables.sample_n_called_spec.html index 7855bc254..0af6d66b6 100644 --- a/latest/generated/sgkit.variables.sample_n_called_spec.html +++ b/latest/generated/sgkit.variables.sample_n_called_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.sample_n_called_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.sample_n_called_spec - - +

    diff --git a/latest/generated/sgkit.variables.sample_n_het_spec.html b/latest/generated/sgkit.variables.sample_n_het_spec.html index 870f917ba..1d52ae58f 100644 --- a/latest/generated/sgkit.variables.sample_n_het_spec.html +++ b/latest/generated/sgkit.variables.sample_n_het_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html b/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html index 9c8e06544..3229d85f0 100644 --- a/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html +++ b/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html b/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html index f346e465b..4c0ab41e1 100644 --- a/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html +++ b/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_n_non_ref_spec.html b/latest/generated/sgkit.variables.sample_n_non_ref_spec.html index 712c5d7a0..e5f1536cf 100644 --- a/latest/generated/sgkit.variables.sample_n_non_ref_spec.html +++ b/latest/generated/sgkit.variables.sample_n_non_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_component_spec.html b/latest/generated/sgkit.variables.sample_pca_component_spec.html index 8865b3cee..49dbfc67e 100644 --- a/latest/generated/sgkit.variables.sample_pca_component_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_component_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html b/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html index 3ea20d4c8..c656b31a2 100644 --- a/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html b/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html index 62e1747bc..4ac626ab1 100644 --- a/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_loading_spec.html b/latest/generated/sgkit.variables.sample_pca_loading_spec.html index 7c938e0d9..a2fb1d16d 100644 --- a/latest/generated/sgkit.variables.sample_pca_loading_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_loading_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_projection_spec.html b/latest/generated/sgkit.variables.sample_pca_projection_spec.html index ad7ee6d3a..ccbcc3dc4 100644 --- a/latest/generated/sgkit.variables.sample_pca_projection_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_projection_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_ploidy_spec.html b/latest/generated/sgkit.variables.sample_ploidy_spec.html index 9d60e7ea6..96500b348 100644 --- a/latest/generated/sgkit.variables.sample_ploidy_spec.html +++ b/latest/generated/sgkit.variables.sample_ploidy_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Fst_spec.html b/latest/generated/sgkit.variables.stat_Fst_spec.html index a5cf66dd9..bd2faa878 100644 --- a/latest/generated/sgkit.variables.stat_Fst_spec.html +++ b/latest/generated/sgkit.variables.stat_Fst_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_Fst_spec#

    -sgkit.variables.stat_Fst_spec = ArrayLikeSpec(default_name='stat_Fst', __doc__='Fixation index (Fst) between pairs of cohorts.', kind='f', ndim=3, dims=({'variants', 'windows'}, 'cohorts_0', 'cohorts_1'))#
    +sgkit.variables.stat_Fst_spec = ArrayLikeSpec(default_name='stat_Fst', __doc__='Fixation index (Fst) between pairs of cohorts.', kind='f', ndim=3, dims=({'windows', 'variants'}, 'cohorts_0', 'cohorts_1'))#

    Fixation index (Fst) between pairs of cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_Garud_h123_spec.html b/latest/generated/sgkit.variables.stat_Garud_h123_spec.html index a7264f5e5..78d6b0b27 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h123_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h123_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_Garud_h123_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.stat_Garud_h123_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_Garud_h12_spec.html b/latest/generated/sgkit.variables.stat_Garud_h12_spec.html index 2c539d2d4..341ca38c8 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h12_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h12_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Garud_h1_spec.html b/latest/generated/sgkit.variables.stat_Garud_h1_spec.html index e550af086..b43c293e0 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h1_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h1_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html b/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html index 0012fd0a8..d527b262a 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html index a8faba57a..27d71fa03 100644 --- a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html +++ b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html index 34b9aa0f4..301d17102 100644 --- a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html +++ b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html b/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html index 61d6e69f3..be8ebe673 100644 --- a/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html +++ b/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_Tajimas_D_spec#

    -sgkit.variables.stat_Tajimas_D_spec = ArrayLikeSpec(default_name='stat_Tajimas_D', __doc__='Tajima’s D for cohorts.', kind='f', ndim=2, dims=({'variants', 'windows'}, 'cohorts'))#
    +sgkit.variables.stat_Tajimas_D_spec = ArrayLikeSpec(default_name='stat_Tajimas_D', __doc__='Tajima’s D for cohorts.', kind='f', ndim=2, dims=({'windows', 'variants'}, 'cohorts'))#

    Tajima’s D for cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html b/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html index 5b4b2e442..0165cac01 100644 --- a/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html +++ b/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_Weir_Goudet_beta_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.stat_Weir_Goudet_beta_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_divergence_spec.html b/latest/generated/sgkit.variables.stat_divergence_spec.html index 58955148e..bef72d007 100644 --- a/latest/generated/sgkit.variables.stat_divergence_spec.html +++ b/latest/generated/sgkit.variables.stat_divergence_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_divergence_spec#

    -sgkit.variables.stat_divergence_spec = ArrayLikeSpec(default_name='stat_divergence', __doc__='Genetic divergence between pairs of cohorts.', kind='f', ndim=3, dims=({'variants', 'windows'}, 'cohorts_0', 'cohorts_1'))#
    +sgkit.variables.stat_divergence_spec = ArrayLikeSpec(default_name='stat_divergence', __doc__='Genetic divergence between pairs of cohorts.', kind='f', ndim=3, dims=({'windows', 'variants'}, 'cohorts_0', 'cohorts_1'))#

    Genetic divergence between pairs of cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_diversity_spec.html b/latest/generated/sgkit.variables.stat_diversity_spec.html index af0b6f8c6..763ad54aa 100644 --- a/latest/generated/sgkit.variables.stat_diversity_spec.html +++ b/latest/generated/sgkit.variables.stat_diversity_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_diversity_spec#

    -sgkit.variables.stat_diversity_spec = ArrayLikeSpec(default_name='stat_diversity', __doc__='Genetic diversity (also known as "Tajima’s pi") for cohorts.', kind='f', ndim=2, dims=({'variants', 'windows'}, 'cohorts'))#
    +sgkit.variables.stat_diversity_spec = ArrayLikeSpec(default_name='stat_diversity', __doc__='Genetic diversity (also known as "Tajima’s pi") for cohorts.', kind='f', ndim=2, dims=({'windows', 'variants'}, 'cohorts'))#

    Genetic diversity (also known as “Tajima’s pi”) for cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html b/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html index 36d7f69e0..8eb286ab6 100644 --- a/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html +++ b/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_genomic_kinship_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.stat_genomic_kinship_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html b/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html index 7e7e4bfcb..1e38c3644 100644 --- a/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html b/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html index 6c89d1217..0f1bf45c2 100644 --- a/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html b/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html index 2a161794b..982acdf19 100644 --- a/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_identity_by_state_spec.html b/latest/generated/sgkit.variables.stat_identity_by_state_spec.html index a9d3d118a..f6250f8f0 100644 --- a/latest/generated/sgkit.variables.stat_identity_by_state_spec.html +++ b/latest/generated/sgkit.variables.stat_identity_by_state_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html b/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html index 0033d35eb..dee870a48 100644 --- a/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html b/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html index 8a7642813..e2818d47b 100644 --- a/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html +++ b/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_observed_heterozygosity_spec#

    -sgkit.variables.stat_observed_heterozygosity_spec = ArrayLikeSpec(default_name='stat_observed_heterozygosity', __doc__='\nObserved heterozygosity for cohorts.\n', kind='f', ndim=2, dims=({'variants', 'windows'}, 'cohorts'))#
    +sgkit.variables.stat_observed_heterozygosity_spec = ArrayLikeSpec(default_name='stat_observed_heterozygosity', __doc__='\nObserved heterozygosity for cohorts.\n', kind='f', ndim=2, dims=({'windows', 'variants'}, 'cohorts'))#

    Observed heterozygosity for cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_pbs_spec.html b/latest/generated/sgkit.variables.stat_pbs_spec.html index 2a4d4a865..af0c54014 100644 --- a/latest/generated/sgkit.variables.stat_pbs_spec.html +++ b/latest/generated/sgkit.variables.stat_pbs_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_pbs_spec#

    -sgkit.variables.stat_pbs_spec = ArrayLikeSpec(default_name='stat_pbs', __doc__='Population branching statistic for cohort triples.', kind='f', ndim=4, dims=({'variants', 'windows'}, 'cohorts_0', 'cohorts_1', 'cohorts_2'))#
    +sgkit.variables.stat_pbs_spec = ArrayLikeSpec(default_name='stat_pbs', __doc__='Population branching statistic for cohort triples.', kind='f', ndim=4, dims=({'windows', 'variants'}, 'cohorts_0', 'cohorts_1', 'cohorts_2'))#

    Population branching statistic for cohort triples.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html b/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html index f8efabd49..9c71e9a7f 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_pedigree_contribution_spec#

    @@ -758,8 +753,7 @@

    sgkit.variables.stat_pedigree_contribution_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html b/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html index 6a05e846d..fdf8a824a 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html index 3c232edde..519a10b92 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html index f0dc86ef3..9c9df7735 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html index be71e1e46..78b7941d0 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html index 2fdfdae8b..555cb08e5 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.traits_spec.html b/latest/generated/sgkit.variables.traits_spec.html index 580adf33f..bf72183a8 100644 --- a/latest/generated/sgkit.variables.traits_spec.html +++ b/latest/generated/sgkit.variables.traits_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_count_spec.html b/latest/generated/sgkit.variables.variant_allele_count_spec.html index 0968a654b..128debcda 100644 --- a/latest/generated/sgkit.variables.variant_allele_count_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_frequency_spec.html b/latest/generated/sgkit.variables.variant_allele_frequency_spec.html index 06de2870b..86b7592e6 100644 --- a/latest/generated/sgkit.variables.variant_allele_frequency_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_frequency_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_spec.html b/latest/generated/sgkit.variables.variant_allele_spec.html index c5fbdfc91..1d455d29a 100644 --- a/latest/generated/sgkit.variables.variant_allele_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_total_spec.html b/latest/generated/sgkit.variables.variant_allele_total_spec.html index cc2ac0676..6fa798209 100644 --- a/latest/generated/sgkit.variables.variant_allele_total_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_total_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_call_rate_spec.html b/latest/generated/sgkit.variables.variant_call_rate_spec.html index abe49dbf6..646d058e0 100644 --- a/latest/generated/sgkit.variables.variant_call_rate_spec.html +++ b/latest/generated/sgkit.variables.variant_call_rate_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_contig_spec.html b/latest/generated/sgkit.variables.variant_contig_spec.html index a768ee167..3889fc033 100644 --- a/latest/generated/sgkit.variables.variant_contig_spec.html +++ b/latest/generated/sgkit.variables.variant_contig_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.variant_contig_spec#

    -sgkit.variables.variant_contig_spec = ArrayLikeSpec(default_name='variant_contig', __doc__='\nIndex corresponding to contig name for each variant. In some less common\nscenarios, this may also be equivalent to the contig names if the data\ngenerating process used contig names that were also integers.\n', kind={'i', 'u'}, ndim=1, dims=('variants',))#
    +sgkit.variables.variant_contig_spec = ArrayLikeSpec(default_name='variant_contig', __doc__='\nIndex corresponding to contig name for each variant. In some less common\nscenarios, this may also be equivalent to the contig names if the data\ngenerating process used contig names that were also integers.\n', kind={'u', 'i'}, ndim=1, dims=('variants',))#

    Index corresponding to contig name for each variant. In some less common scenarios, this may also be equivalent to the contig names if the data generating process used contig names that were also integers.

    @@ -757,8 +752,7 @@

    sgkit.variables.variant_contig_spec - - +

    diff --git a/latest/generated/sgkit.variables.variant_genotype_count_spec.html b/latest/generated/sgkit.variables.variant_genotype_count_spec.html index dff3aa806..59e939cb9 100644 --- a/latest/generated/sgkit.variables.variant_genotype_count_spec.html +++ b/latest/generated/sgkit.variables.variant_genotype_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.variant_genotype_count_spec#

    -sgkit.variables.variant_genotype_count_spec = ArrayLikeSpec(default_name='variant_genotype_count', __doc__='\nThe number of observations for each possible genotype at each variant.\nCounts are sorted following the ordering defined in the VCF specification.\n\n- For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``\n  (homozygous reference, heterozygous, homozygous alternate).\n- For triallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``,\n  ``02``, ``12``, ``22``\n- For triallelic, triploid genotypes the ordering is  ``000``, ``001``, ``011``,\n  ``111``, ``002``, ``012``, ``112``, ``022``, ``122``, ``222``\n', kind={'i', 'u'}, ndim=2, dims=('variants', 'genotypes'))#
    +sgkit.variables.variant_genotype_count_spec = ArrayLikeSpec(default_name='variant_genotype_count', __doc__='\nThe number of observations for each possible genotype at each variant.\nCounts are sorted following the ordering defined in the VCF specification.\n\n- For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``\n  (homozygous reference, heterozygous, homozygous alternate).\n- For triallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``,\n  ``02``, ``12``, ``22``\n- For triallelic, triploid genotypes the ordering is  ``000``, ``001``, ``011``,\n  ``111``, ``002``, ``012``, ``112``, ``022``, ``122``, ``222``\n', kind={'u', 'i'}, ndim=2, dims=('variants', 'genotypes'))#

    The number of observations for each possible genotype at each variant. Counts are sorted following the ordering defined in the VCF specification.

      @@ -764,8 +759,7 @@

      sgkit.variables.variant_genotype_count_spec - - +

    diff --git a/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html b/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html index 0a78abefd..c9586a3ec 100644 --- a/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html +++ b/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_id_spec.html b/latest/generated/sgkit.variables.variant_id_spec.html index ffe976cfe..17963f0eb 100644 --- a/latest/generated/sgkit.variables.variant_id_spec.html +++ b/latest/generated/sgkit.variables.variant_id_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.variant_id_spec#

    -sgkit.variables.variant_id_spec = ArrayLikeSpec(default_name='variant_id', __doc__='The unique identifier of the variant.', kind={'U', 'S', 'O'}, ndim=1, dims=('variants',))#
    +sgkit.variables.variant_id_spec = ArrayLikeSpec(default_name='variant_id', __doc__='The unique identifier of the variant.', kind={'S', 'U', 'O'}, ndim=1, dims=('variants',))#

    The unique identifier of the variant.

    - - +
    diff --git a/latest/generated/sgkit.variables.variant_linreg_beta_spec.html b/latest/generated/sgkit.variables.variant_linreg_beta_spec.html index 2a2415f19..a87ee01d0 100644 --- a/latest/generated/sgkit.variables.variant_linreg_beta_spec.html +++ b/latest/generated/sgkit.variables.variant_linreg_beta_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.variant_linreg_beta_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.variant_linreg_beta_spec - - +

    diff --git a/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html b/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html index 622408ffd..15f36ab4b 100644 --- a/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html +++ b/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html b/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html index 7116a0b62..142e94bda 100644 --- a/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html +++ b/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_called_spec.html b/latest/generated/sgkit.variables.variant_n_called_spec.html index 0fd95122f..659a1aeef 100644 --- a/latest/generated/sgkit.variables.variant_n_called_spec.html +++ b/latest/generated/sgkit.variables.variant_n_called_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_het_spec.html b/latest/generated/sgkit.variables.variant_n_het_spec.html index de052a7f3..b48cc516f 100644 --- a/latest/generated/sgkit.variables.variant_n_het_spec.html +++ b/latest/generated/sgkit.variables.variant_n_het_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html b/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html index 8acd2a98f..1e9d24506 100644 --- a/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html +++ b/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html b/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html index dda31c706..da45db9c5 100644 --- a/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html +++ b/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_non_ref_spec.html b/latest/generated/sgkit.variables.variant_n_non_ref_spec.html index 1c01012a0..dfd28813c 100644 --- a/latest/generated/sgkit.variables.variant_n_non_ref_spec.html +++ b/latest/generated/sgkit.variables.variant_n_non_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_ploidy_spec.html b/latest/generated/sgkit.variables.variant_ploidy_spec.html index c9b470b5a..734f64de2 100644 --- a/latest/generated/sgkit.variables.variant_ploidy_spec.html +++ b/latest/generated/sgkit.variables.variant_ploidy_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_position_spec.html b/latest/generated/sgkit.variables.variant_position_spec.html index 4136ad84e..d5b6df37f 100644 --- a/latest/generated/sgkit.variables.variant_position_spec.html +++ b/latest/generated/sgkit.variables.variant_position_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_score_spec.html b/latest/generated/sgkit.variables.variant_score_spec.html index 4078f4f16..15b49029f 100644 --- a/latest/generated/sgkit.variables.variant_score_spec.html +++ b/latest/generated/sgkit.variables.variant_score_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.window_contig_spec.html b/latest/generated/sgkit.variables.window_contig_spec.html index 8deb83234..04b12fe3b 100644 --- a/latest/generated/sgkit.variables.window_contig_spec.html +++ b/latest/generated/sgkit.variables.window_contig_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.window_start_spec.html b/latest/generated/sgkit.variables.window_start_spec.html index 9d0ad828e..67a3dba1b 100644 --- a/latest/generated/sgkit.variables.window_start_spec.html +++ b/latest/generated/sgkit.variables.window_start_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.window_stop_spec.html b/latest/generated/sgkit.variables.window_stop_spec.html index f9557fb4b..ef11b4978 100644 --- a/latest/generated/sgkit.variables.window_stop_spec.html +++ b/latest/generated/sgkit.variables.window_stop_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variant_stats.html b/latest/generated/sgkit.variant_stats.html index ff6cdc443..4a3445485 100644 --- a/latest/generated/sgkit.variant_stats.html +++ b/latest/generated/sgkit.variant_stats.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_genome.html b/latest/generated/sgkit.window_by_genome.html index 2f7b71cc7..aef92e860 100644 --- a/latest/generated/sgkit.window_by_genome.html +++ b/latest/generated/sgkit.window_by_genome.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_interval.html b/latest/generated/sgkit.window_by_interval.html index 947ac65ea..6eb45a1ec 100644 --- a/latest/generated/sgkit.window_by_interval.html +++ b/latest/generated/sgkit.window_by_interval.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_position.html b/latest/generated/sgkit.window_by_position.html index 2645b9fdc..9c91737d8 100644 --- a/latest/generated/sgkit.window_by_position.html +++ b/latest/generated/sgkit.window_by_position.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_variant.html b/latest/generated/sgkit.window_by_variant.html index b4467e78b..fed960c11 100644 --- a/latest/generated/sgkit.window_by_variant.html +++ b/latest/generated/sgkit.window_by_variant.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/getting_started.html b/latest/getting_started.html index 12fc4aaaf..6560deea4 100644 --- a/latest/getting_started.html +++ b/latest/getting_started.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@ diff --git a/latest/how_do_i.html b/latest/how_do_i.html index 9daa63deb..f16cca307 100644 --- a/latest/how_do_i.html +++ b/latest/how_do_i.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@ diff --git a/latest/index.html b/latest/index.html index d925c2e48..5128e56f8 100644 --- a/latest/index.html +++ b/latest/index.html @@ -55,13 +55,9 @@ - - + - - - - + @@ -515,8 +511,7 @@ diff --git a/latest/news.html b/latest/news.html index 02f8c6537..180a233a3 100644 --- a/latest/news.html +++ b/latest/news.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@ diff --git a/latest/news/introducing_sgkit.html b/latest/news/introducing_sgkit.html index ec506681c..cbe66b77a 100644 --- a/latest/news/introducing_sgkit.html +++ b/latest/news/introducing_sgkit.html @@ -54,13 +54,9 @@ - - + - - - - + @@ -540,8 +536,7 @@
    - -
    +

    Introducing sgkit#

    The sgkit team is pleased to announce the release of sgkit 0.5.0! This release adds support for the VCF Zarr specification, which describes an encoding of VCF data in chunked-columnar form using the Zarr format.

    With this release, we also introduce our news page, where we will announce future releases and provide other relevant updates for the sgkit project.

    @@ -551,10 +546,7 @@

    Introducing sgkit - - - - +
    @@ -564,8 +556,6 @@

    Introducing sgkit - - + - - - - + diff --git a/latest/searchindex.js b/latest/searchindex.js index f6749e492..4460b9a82 100644 --- a/latest/searchindex.js +++ b/latest/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["about", "api", "changelog", "contributing", "examples/gwas_tutorial", "examples/index", "examples/relatedness_tutorial", "generated/sgkit.Fst", "generated/sgkit.Garud_H", "generated/sgkit.Tajimas_D", "generated/sgkit.Weir_Goudet_beta", "generated/sgkit.call_allele_frequencies", "generated/sgkit.cohort_allele_frequencies", "generated/sgkit.convert_call_to_index", "generated/sgkit.convert_probability_to_call", "generated/sgkit.count_call_alleles", "generated/sgkit.count_cohort_alleles", "generated/sgkit.count_variant_alleles", "generated/sgkit.count_variant_genotypes", "generated/sgkit.display_genotypes", "generated/sgkit.display_pedigree", "generated/sgkit.divergence", "generated/sgkit.diversity", "generated/sgkit.filter_partial_calls", "generated/sgkit.genee", "generated/sgkit.genomic_relationship", "generated/sgkit.gwas_linear_regression", "generated/sgkit.hardy_weinberg_test", "generated/sgkit.hybrid_inverse_relationship", "generated/sgkit.hybrid_relationship", "generated/sgkit.identity_by_state", "generated/sgkit.individual_heterozygosity", "generated/sgkit.infer_call_ploidy", "generated/sgkit.infer_sample_ploidy", "generated/sgkit.infer_variant_ploidy", "generated/sgkit.invert_relationship_matrix", "generated/sgkit.io.bgen.bgen_to_zarr", "generated/sgkit.io.bgen.read_bgen", "generated/sgkit.io.bgen.rechunk_bgen", "generated/sgkit.io.plink.plink_to_zarr", "generated/sgkit.io.plink.read_plink", "generated/sgkit.io.plink.write_plink", "generated/sgkit.io.plink.zarr_to_plink", "generated/sgkit.io.vcf.concat_zarrs", "generated/sgkit.io.vcf.partition_into_regions", "generated/sgkit.io.vcf.read_vcf", "generated/sgkit.io.vcf.vcf_to_zarr", "generated/sgkit.io.vcf.vcf_to_zarrs", "generated/sgkit.io.vcf.write_vcf", "generated/sgkit.io.vcf.zarr_array_sizes", "generated/sgkit.io.vcf.zarr_to_vcf", "generated/sgkit.ld_matrix", "generated/sgkit.ld_prune", "generated/sgkit.load_dataset", "generated/sgkit.maximal_independent_set", "generated/sgkit.observed_heterozygosity", "generated/sgkit.pairwise_distance", "generated/sgkit.parent_indices", "generated/sgkit.pbs", "generated/sgkit.pc_relate", "generated/sgkit.pedigree_contribution", "generated/sgkit.pedigree_inbreeding", "generated/sgkit.pedigree_inverse_kinship", "generated/sgkit.pedigree_kinship", "generated/sgkit.pedigree_sel", "generated/sgkit.read_scikit_allel_vcfzarr", "generated/sgkit.regenie", "generated/sgkit.sample_stats", "generated/sgkit.save_dataset", "generated/sgkit.simulate_genedrop", "generated/sgkit.simulate_genotype_call_dataset", "generated/sgkit.variables.call_allele_count_spec", "generated/sgkit.variables.call_allele_frequency_spec", "generated/sgkit.variables.call_dosage_mask_spec", "generated/sgkit.variables.call_dosage_spec", "generated/sgkit.variables.call_genotype_complete_mask_spec", "generated/sgkit.variables.call_genotype_complete_spec", "generated/sgkit.variables.call_genotype_fill_spec", "generated/sgkit.variables.call_genotype_index_mask_spec", "generated/sgkit.variables.call_genotype_index_spec", "generated/sgkit.variables.call_genotype_mask_spec", "generated/sgkit.variables.call_genotype_phased_spec", "generated/sgkit.variables.call_genotype_probability_mask_spec", "generated/sgkit.variables.call_genotype_probability_spec", "generated/sgkit.variables.call_genotype_spec", "generated/sgkit.variables.call_heterozygosity_spec", "generated/sgkit.variables.call_ploidy_spec", "generated/sgkit.variables.cohort_allele_count_spec", "generated/sgkit.variables.cohort_allele_frequency_spec", "generated/sgkit.variables.covariates_spec", "generated/sgkit.variables.interval_contig_name_spec", "generated/sgkit.variables.interval_start_spec", "generated/sgkit.variables.interval_stop_spec", "generated/sgkit.variables.ld_prune_index_to_drop_spec", "generated/sgkit.variables.parent_id_spec", "generated/sgkit.variables.parent_spec", "generated/sgkit.variables.pc_relate_phi_spec", "generated/sgkit.variables.regenie_base_prediction_spec", "generated/sgkit.variables.regenie_loco_prediction_spec", "generated/sgkit.variables.regenie_meta_prediction_spec", "generated/sgkit.variables.sample_call_rate_spec", "generated/sgkit.variables.sample_cohort_spec", "generated/sgkit.variables.sample_id_spec", "generated/sgkit.variables.sample_n_called_spec", "generated/sgkit.variables.sample_n_het_spec", "generated/sgkit.variables.sample_n_hom_alt_spec", "generated/sgkit.variables.sample_n_hom_ref_spec", "generated/sgkit.variables.sample_n_non_ref_spec", "generated/sgkit.variables.sample_pca_component_spec", "generated/sgkit.variables.sample_pca_explained_variance_ratio_spec", "generated/sgkit.variables.sample_pca_explained_variance_spec", "generated/sgkit.variables.sample_pca_loading_spec", "generated/sgkit.variables.sample_pca_projection_spec", "generated/sgkit.variables.sample_ploidy_spec", "generated/sgkit.variables.stat_Fst_spec", "generated/sgkit.variables.stat_Garud_h123_spec", "generated/sgkit.variables.stat_Garud_h12_spec", "generated/sgkit.variables.stat_Garud_h1_spec", "generated/sgkit.variables.stat_Garud_h2_h1_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec", "generated/sgkit.variables.stat_Tajimas_D_spec", "generated/sgkit.variables.stat_Weir_Goudet_beta_spec", "generated/sgkit.variables.stat_divergence_spec", "generated/sgkit.variables.stat_diversity_spec", "generated/sgkit.variables.stat_genomic_kinship_spec", "generated/sgkit.variables.stat_genomic_relationship_spec", "generated/sgkit.variables.stat_hybrid_inverse_relationship_spec", "generated/sgkit.variables.stat_hybrid_relationship_spec", "generated/sgkit.variables.stat_identity_by_state_spec", "generated/sgkit.variables.stat_inverse_relationship_spec", "generated/sgkit.variables.stat_observed_heterozygosity_spec", "generated/sgkit.variables.stat_pbs_spec", "generated/sgkit.variables.stat_pedigree_contribution_spec", "generated/sgkit.variables.stat_pedigree_inbreeding_spec", "generated/sgkit.variables.stat_pedigree_inverse_kinship_spec", "generated/sgkit.variables.stat_pedigree_inverse_relationship_spec", "generated/sgkit.variables.stat_pedigree_kinship_spec", "generated/sgkit.variables.stat_pedigree_relationship_spec", "generated/sgkit.variables.traits_spec", "generated/sgkit.variables.variant_allele_count_spec", "generated/sgkit.variables.variant_allele_frequency_spec", "generated/sgkit.variables.variant_allele_spec", "generated/sgkit.variables.variant_allele_total_spec", "generated/sgkit.variables.variant_call_rate_spec", "generated/sgkit.variables.variant_contig_spec", "generated/sgkit.variables.variant_genotype_count_spec", "generated/sgkit.variables.variant_hwe_p_value_spec", "generated/sgkit.variables.variant_id_spec", "generated/sgkit.variables.variant_linreg_beta_spec", "generated/sgkit.variables.variant_linreg_p_value_spec", "generated/sgkit.variables.variant_linreg_t_value_spec", "generated/sgkit.variables.variant_n_called_spec", "generated/sgkit.variables.variant_n_het_spec", "generated/sgkit.variables.variant_n_hom_alt_spec", "generated/sgkit.variables.variant_n_hom_ref_spec", "generated/sgkit.variables.variant_n_non_ref_spec", "generated/sgkit.variables.variant_ploidy_spec", "generated/sgkit.variables.variant_position_spec", "generated/sgkit.variables.variant_score_spec", "generated/sgkit.variables.window_contig_spec", "generated/sgkit.variables.window_start_spec", "generated/sgkit.variables.window_stop_spec", "generated/sgkit.variant_stats", "generated/sgkit.window_by_genome", "generated/sgkit.window_by_interval", "generated/sgkit.window_by_position", "generated/sgkit.window_by_variant", "getting_started", "how_do_i", "index", "news", "news/introducing_sgkit", "user_guide", "vcf"], "filenames": ["about.rst", "api.rst", "changelog.rst", "contributing.rst", "examples/gwas_tutorial.ipynb", "examples/index.rst", "examples/relatedness_tutorial.ipynb", "generated/sgkit.Fst.rst", "generated/sgkit.Garud_H.rst", "generated/sgkit.Tajimas_D.rst", "generated/sgkit.Weir_Goudet_beta.rst", "generated/sgkit.call_allele_frequencies.rst", "generated/sgkit.cohort_allele_frequencies.rst", "generated/sgkit.convert_call_to_index.rst", "generated/sgkit.convert_probability_to_call.rst", "generated/sgkit.count_call_alleles.rst", "generated/sgkit.count_cohort_alleles.rst", "generated/sgkit.count_variant_alleles.rst", "generated/sgkit.count_variant_genotypes.rst", "generated/sgkit.display_genotypes.rst", "generated/sgkit.display_pedigree.rst", "generated/sgkit.divergence.rst", "generated/sgkit.diversity.rst", "generated/sgkit.filter_partial_calls.rst", "generated/sgkit.genee.rst", "generated/sgkit.genomic_relationship.rst", "generated/sgkit.gwas_linear_regression.rst", "generated/sgkit.hardy_weinberg_test.rst", "generated/sgkit.hybrid_inverse_relationship.rst", "generated/sgkit.hybrid_relationship.rst", "generated/sgkit.identity_by_state.rst", "generated/sgkit.individual_heterozygosity.rst", "generated/sgkit.infer_call_ploidy.rst", "generated/sgkit.infer_sample_ploidy.rst", "generated/sgkit.infer_variant_ploidy.rst", "generated/sgkit.invert_relationship_matrix.rst", "generated/sgkit.io.bgen.bgen_to_zarr.rst", "generated/sgkit.io.bgen.read_bgen.rst", "generated/sgkit.io.bgen.rechunk_bgen.rst", "generated/sgkit.io.plink.plink_to_zarr.rst", "generated/sgkit.io.plink.read_plink.rst", "generated/sgkit.io.plink.write_plink.rst", "generated/sgkit.io.plink.zarr_to_plink.rst", "generated/sgkit.io.vcf.concat_zarrs.rst", "generated/sgkit.io.vcf.partition_into_regions.rst", "generated/sgkit.io.vcf.read_vcf.rst", "generated/sgkit.io.vcf.vcf_to_zarr.rst", 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36, 37, 39, 40, 45, 46, 47, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 89, 90, 139, 145, 163, 165, 166, 167, 168, 169, 174], "singular": [1, 62, 108], "exampl": [1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 21, 22, 23, 25, 28, 29, 30, 31, 35, 45, 46, 47, 48, 52, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66, 69, 139, 164, 166, 167, 168, 170, 173], "genotype_count": [1, 2, 27], "add": [2, 3, 4, 26, 63, 66, 70, 164, 165, 166, 167, 169, 171, 172], "match": [2, 4, 6, 25, 30, 36, 69, 90, 94, 119, 120], "method": [2, 6, 7, 8, 9, 13, 17, 18, 21, 22, 25, 26, 28, 29, 30, 51, 52, 54, 58, 59, 60, 61, 62, 63, 67, 69, 70, 163, 170, 172, 174], "identity_by_st": [2, 10], "timothymillar": 2, "pr": 2, "1229": 2, "gh": [2, 8], "1227": 2, "read": [2, 3, 4, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 49, 65, 69, 168, 170, 172], "vcf": [2, 6, 19, 65, 79, 146, 168, 170, 171, 172], "favour": 2, "tomwhit": 2, "1233": 2, "1232": 2, "pin": [2, 3], "1230": 2, "numpi": [2, 3, 4, 6, 7, 8, 9, 12, 16, 21, 22, 28, 29, 52, 55, 56, 58, 63, 66, 69, 168, 173], "cbgen": [2, 172], "1228": 2, "1225": 2, "pedigree_contribut": 2, "1093": 2, "963": 2, "pedigree_sel": 2, "1087": 2, "1033": 2, "endelman": [2, 25], "jannink": [2, 25], "estim": [2, 7, 10, 24, 25, 28, 29, 30, 59, 60, 61, 62, 63, 66, 99, 137], "genomic_relationship": [2, 6, 28, 29], "1100": 2, "1062": 2, "display_pedigre": 2, "1104": 2, "1097": 2, "option": [2, 3, 4, 7, 8, 19, 20, 25, 27, 28, 29, 35, 36, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 58, 60, 62, 63, 64, 65, 66, 68, 69, 70, 166, 167, 168, 173, 174], "count": [2, 4, 9, 15, 16, 17, 18, 21, 22, 25, 27, 40, 67, 71, 74, 79, 87, 140, 146, 163, 168, 173], "variant": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 30, 31, 33, 34, 36, 37, 38, 39, 40, 43, 45, 46, 47, 48, 49, 51, 52, 54, 55, 58, 59, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 93, 98, 100, 103, 104, 105, 106, 107, 108, 111, 113, 114, 121, 123, 124, 131, 132, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 161, 162, 163, 165, 166, 167, 168, 170, 172, 173, 174], "directli": [2, 3, 4, 17, 30, 36, 44, 56, 61, 168, 173], "call": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 45, 46, 47, 55, 56, 58, 59, 67, 69, 70, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 86, 100, 103, 104, 105, 106, 107, 113, 144, 152, 153, 154, 155, 156, 157, 163, 164, 165, 166, 167, 168, 169, 173, 174], "genotyp": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 45, 46, 47, 51, 52, 55, 58, 59, 65, 66, 67, 69, 70, 76, 77, 78, 79, 82, 83, 84, 85, 86, 100, 103, 113, 144, 146, 152, 157, 163, 164, 165, 166, 167, 168, 170, 173, 174], "count_variant_allel": [2, 9, 163, 168, 173], "1119": 2, "1116": 2, "simulate_genedrop": 2, "1139": 2, "1107": 2, "perform": [2, 3, 37, 38, 39, 40, 168, 173, 174], "variant_stat": [2, 4, 168, 169, 173], "sample_stat": [2, 4, 169], "error": [2, 6, 35, 45, 46, 66, 168, 169, 173, 174], "miss": [2, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 23, 25, 30, 40, 41, 45, 46, 47, 56, 57, 59, 64, 67, 70, 71, 72, 73, 74, 75, 76, 78, 79, 80, 82, 84, 88, 140, 163, 170, 173], "handl": [2, 3, 168, 174], "valu": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 43, 44, 45, 46, 47, 48, 49, 51, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 69, 70, 71, 72, 73, 74, 75, 77, 79, 80, 82, 84, 88, 95, 101, 110, 111, 120, 125, 130, 133, 137, 140, 147, 149, 150, 161, 162, 164, 165, 166, 167, 168, 170, 173, 174], "most": [2, 3, 6, 51, 52, 59, 168, 173], "field": [2, 24, 38, 39, 40, 41, 45, 46, 47, 48, 51, 65, 70, 174], "were": [2, 3, 4, 6, 119, 145, 170], "mark": 2, "correspond": [2, 3, 4, 6, 11, 12, 15, 16, 17, 25, 27, 28, 29, 39, 40, 45, 46, 47, 48, 59, 64, 65, 71, 72, 78, 79, 88, 89, 139, 140, 145, 168, 169], "fill": [2, 4, 32, 33, 34, 45, 46, 47, 77], "string": [2, 4, 6, 36, 38, 39, 40, 44, 45, 46, 47, 49, 174], "store": [2, 4, 6, 36, 38, 39, 42, 43, 45, 46, 47, 50, 53, 68, 172, 173, 174], "empti": 2, "rather": [2, 3, 4, 6, 24, 28, 29, 173, 174], "than": [2, 3, 4, 6, 14, 19, 24, 28, 29, 32, 36, 37, 44, 45, 46, 47, 48, 59, 61, 62, 63, 65, 69, 173, 174], "similarli": [2, 173], "integ": [2, 4, 6, 13, 36, 37, 39, 40, 44, 45, 46, 47, 57, 63, 64, 65, 69, 79, 145, 168, 169, 173, 174], "int": [2, 8, 19, 25, 27, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 49, 56, 58, 64, 66, 70, 166, 167, 174], "jeromekelleh": 2, "1190": 2, "1192": 2, "max_str_len": 2, "util": [2, 4, 28, 29, 168, 170, 173], "return": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "python": [2, 4, 6, 48, 165, 168, 174], "arrai": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 37, 39, 40, 45, 46, 47, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66, 69, 79, 89, 112, 139, 166, 167, 169, 170, 173, 174], "scalar": [2, 168], "1086": 2, "1085": 2, "turn": 2, "off": [2, 168, 174], "numba": [2, 48], "cach": 2, "default": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "1191": 2, "1156": 2, "xarrai": [2, 3, 4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 28, 29, 35, 45, 46, 47, 53, 55, 58, 66, 68, 70, 164, 166, 167, 168, 169, 170, 172, 173, 174], "repr": [2, 169], "doctest": [2, 3], "1205": 2, "1204": 2, "avoid": [2, 3, 4, 6, 35, 45, 46, 51, 52, 168, 169, 174], "disabl": [2, 14], "jit": [2, 173], "guvectoris": 2, "1199": 2, "1194": 2, "tutori": [2, 168], "relationship": [2, 25, 28, 29, 35, 59, 61, 62, 63, 69, 126, 127, 128, 130, 136, 138], "matric": [2, 28, 29], "1072": 2, "956": 2, "pairwise_dist": 2, "doc": [2, 3, 37, 39, 40], "benjefferi": 2, "1145": 2, "1142": 2, "format": [2, 3, 4, 6, 19, 40, 45, 46, 47, 65, 168, 171, 172, 173, 174], "matrix": [2, 6, 10, 25, 28, 29, 30, 35, 51, 52, 54, 56, 59, 61, 62, 63, 69, 96, 108, 110, 125, 126, 127, 128, 130, 133, 135, 136, 138, 159], "pairwis": [2, 6, 10, 25, 28, 29, 30, 56, 59, 63, 122, 129, 137], "1148": 2, "1147": 2, "io": [2, 3, 4, 6, 14, 65, 66, 170, 173, 174], "plink": [2, 6, 54, 168, 172], "write_plink": [2, 42, 173], "1003": 2, "926": [2, 168], "phase": [2, 4, 19, 36, 65, 70, 81], "simulate_genotype_call_dataset": [2, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 52, 55, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 173], "1022": 2, "973": 2, "plink_to_zarr": 2, "zarr_to_plink": [2, 173], "conveni": [2, 4, 26, 36, 39, 42, 45, 50, 70, 168, 173], "1047": 2, "1004": 2, "convert_call_to_index": [2, 173], "1050": 2, "1048": 2, "read_chunk_length": [2, 46, 47], "vcf_to_zarr": [2, 4, 43, 45, 48, 65, 173, 174], "These": [2, 3, 6, 25, 27, 66, 110, 111, 168, 173], "reduc": [2, 46, 47, 56, 168], "memori": [2, 4, 36, 37, 38, 39, 40, 45, 46, 47, 48, 54, 61, 168, 169, 173, 174], "usag": [2, 4, 46, 47, 61, 168, 170], "larg": [2, 3, 26, 30, 45, 46, 47, 51, 52, 168, 170, 173, 174], "sampl": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 45, 46, 47, 48, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 89, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 112, 113, 119, 120, 122, 129, 133, 134, 137, 139, 144, 152, 153, 154, 155, 156, 157, 163, 168, 170, 172, 173, 174], "chunk_length": [2, 36, 38, 43, 45, 46, 47, 174], "1044": 2, "1042": 2, "retain_temp_fil": [2, 46], "1046": 2, "1036": 2, "read_vcf": 2, "1052": 2, "hybrid_relationship": [2, 6, 28], "hybrid_inverse_relationship": [2, 29], "invert_relationship_matrix": [2, 6, 28, 29], "1053": 2, "993": [2, 6], "zarr_array_s": 2, "determin": [2, 3, 7, 37, 49, 56, 168], "size": [2, 4, 6, 7, 8, 9, 12, 16, 18, 21, 22, 24, 25, 26, 35, 37, 39, 40, 44, 45, 46, 47, 48, 49, 52, 55, 56, 58, 63, 66, 79, 164, 166, 167, 168, 169, 170, 173], "storag": [2, 4, 6, 39, 43, 44, 45, 46, 47, 49, 53, 68, 168, 170, 173], "1073": 2, "734": 2, "skipna": [2, 25, 30], "1078": 2, "1076": 2, "additional_variant_field": [2, 70], "1056": 2, "header": [2, 45, 46, 47, 48, 50, 65], "when": [2, 3, 6, 17, 26, 28, 29, 30, 36, 37, 38, 39, 40, 45, 46, 47, 55, 63, 67, 69, 70, 120, 159, 163, 168, 173, 174], "write": [2, 3, 4, 6, 46, 48, 170, 172, 174], "write_vcf": [2, 50, 173], "zarr_to_vcf": [2, 48, 173], "previous": [2, 3], "dataset": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 84, 89, 120, 139, 163, 164, 165, 166, 167, 168, 170], "had": [2, 6], "contain": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 39, 40, 41, 47, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 98, 130, 139, 163, 164, 165, 166, 167, 168, 173], "vcf_header": [2, 48, 50], "attribut": [2, 4, 6, 20, 48, 50, 90, 168, 169, 173, 174], "1021": 2, "1020": 2, "contig": [2, 4, 37, 39, 40, 66, 70, 90, 98, 145, 160, 165, 166, 167, 168, 169, 173, 174], "contig_id": [2, 4, 168, 169], "filter": [2, 4, 6, 45, 46, 47, 59, 168, 170, 174], "filter_id": [2, 4], "duplic": [2, 3, 69], "inform": [2, 3, 6, 7, 9, 19, 21, 22, 28, 29, 37, 39, 40, 45, 46, 47, 52, 58, 65, 165, 166, 167, 168, 173, 174], "which": [2, 3, 4, 6, 10, 21, 23, 25, 27, 28, 29, 30, 35, 36, 38, 41, 44, 45, 46, 47, 49, 51, 52, 56, 61, 62, 63, 65, 66, 69, 73, 75, 76, 78, 80, 82, 120, 130, 133, 166, 168, 170, 171, 172, 173, 174], "now": [2, 3, 4, 6, 56, 168, 172, 173], "remov": [2, 4, 6, 23, 25, 26, 36, 38, 52, 57, 66, 169], "futur": [2, 3, 6, 172, 173], "releas": [2, 3, 4, 6, 171, 172, 174], "1054": 2, "1035": 2, "paramet": [2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 173, 174], "founder_indic": [2, 63], "pedigree_kinship": [2, 6], "instead": [2, 6, 36, 38, 63], "founder_kinship": [2, 63], "expect": [2, 4, 6, 60, 61, 63, 133, 134, 137, 173, 174], "full": [2, 4, 6, 28, 29, 39, 40, 41, 42, 59, 61, 63, 168, 173, 174], "kinship": [2, 6, 10, 59, 61, 62, 63, 96, 125, 135, 137, 172], "founder": [2, 6, 61, 62, 63, 69], "ignor": [2, 4, 6, 29, 45, 46, 48, 49, 55, 56, 63, 66, 67, 98, 163, 168], "1075": 2, "1061": 2, "scale": [2, 6, 10, 28, 29, 111, 168, 170, 173, 174], "number": [2, 3, 4, 6, 15, 16, 17, 18, 19, 25, 27, 32, 33, 34, 36, 38, 41, 44, 45, 46, 47, 59, 63, 65, 66, 67, 69, 70, 71, 103, 104, 105, 106, 107, 120, 140, 143, 146, 152, 153, 154, 155, 156, 163, 166, 167, 168, 173, 174], "1028": 2, "1026": 2, "1027": 2, "import": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 28, 29, 30, 31, 35, 37, 39, 40, 48, 52, 55, 56, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 170, 173, 174], "much": [2, 4, 6, 36, 37, 38, 174], "faster": [2, 4, 63, 173, 174], "due": [2, 3, 6, 60, 168, 174], "defer": 2, "compil": [2, 168, 173], "1039": [2, 3], "939": 2, "wa": [2, 3, 25, 35, 38, 172], "output": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 43, 45, 46, 47, 48, 50, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 173, 174], "file": [2, 3, 4, 6, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 65, 68, 170, 172, 173], "temp_chunk_length": [2, 36, 45, 46, 174], "chunk": [2, 4, 6, 7, 9, 21, 22, 35, 36, 37, 38, 39, 40, 43, 45, 46, 47, 48, 58, 60, 68, 169, 170, 171, 172, 173], "ha": [2, 3, 4, 6, 14, 17, 36, 44, 61, 62, 63, 69, 70, 168, 173, 174], "been": [2, 3, 4, 6, 17, 44, 48, 52, 61, 166, 173], "so": [2, 3, 4, 6, 25, 36, 38, 44, 45, 46, 47, 48, 61, 62, 63, 66, 70, 165, 168, 169, 173, 174], "fail": [2, 37], "zerodivisionerror": 2, "1069": 2, "1068": 2, "correct": [2, 3, 6, 10, 168], "mix": [2, 4, 13, 18, 26, 32, 61, 62, 63, 67, 69, 77, 84, 163, 170], "ploidi": [2, 4, 6, 13, 14, 18, 25, 27, 31, 32, 33, 34, 40, 41, 45, 46, 47, 52, 59, 60, 61, 62, 63, 65, 67, 69, 70, 75, 76, 77, 80, 84, 86, 113, 120, 157, 163, 168, 169, 170, 173], "display_genotyp": [2, 4, 10, 11, 12, 13, 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"sgkit.variables.call_genotype_mask_spec": [[80, "sgkit-variables-call-genotype-mask-spec"]], "sgkit.variables.call_genotype_phased_spec": [[81, "sgkit-variables-call-genotype-phased-spec"]], "sgkit.variables.call_genotype_probability_mask_spec": [[82, "sgkit-variables-call-genotype-probability-mask-spec"]], "sgkit.variables.call_genotype_probability_spec": [[83, "sgkit-variables-call-genotype-probability-spec"]], "sgkit.variables.call_genotype_spec": [[84, "sgkit-variables-call-genotype-spec"]], "sgkit.variables.call_heterozygosity_spec": [[85, "sgkit-variables-call-heterozygosity-spec"]], "sgkit.variables.call_ploidy_spec": [[86, "sgkit-variables-call-ploidy-spec"]], "sgkit.variables.cohort_allele_count_spec": [[87, "sgkit-variables-cohort-allele-count-spec"]], "sgkit.variables.cohort_allele_frequency_spec": [[88, "sgkit-variables-cohort-allele-frequency-spec"]], "sgkit.variables.covariates_spec": [[89, "sgkit-variables-covariates-spec"]], "sgkit.variables.interval_contig_name_spec": [[90, "sgkit-variables-interval-contig-name-spec"]], "sgkit.variables.interval_start_spec": [[91, "sgkit-variables-interval-start-spec"]], "sgkit.variables.interval_stop_spec": [[92, "sgkit-variables-interval-stop-spec"]], "sgkit.variables.ld_prune_index_to_drop_spec": [[93, "sgkit-variables-ld-prune-index-to-drop-spec"]], "sgkit.variables.parent_id_spec": [[94, "sgkit-variables-parent-id-spec"]], "sgkit.variables.parent_spec": [[95, "sgkit-variables-parent-spec"]], "sgkit.variables.pc_relate_phi_spec": [[96, "sgkit-variables-pc-relate-phi-spec"]], "sgkit.variables.regenie_base_prediction_spec": [[97, "sgkit-variables-regenie-base-prediction-spec"]], "sgkit.variables.regenie_loco_prediction_spec": [[98, "sgkit-variables-regenie-loco-prediction-spec"]], "sgkit.variables.regenie_meta_prediction_spec": [[99, "sgkit-variables-regenie-meta-prediction-spec"]], "sgkit.variables.sample_call_rate_spec": [[100, "sgkit-variables-sample-call-rate-spec"]], "sgkit.variables.sample_cohort_spec": [[101, "sgkit-variables-sample-cohort-spec"]], "sgkit.variables.sample_id_spec": [[102, "sgkit-variables-sample-id-spec"]], "sgkit.variables.sample_n_called_spec": [[103, "sgkit-variables-sample-n-called-spec"]], "sgkit.variables.sample_n_het_spec": [[104, "sgkit-variables-sample-n-het-spec"]], "sgkit.variables.sample_n_hom_alt_spec": [[105, "sgkit-variables-sample-n-hom-alt-spec"]], "sgkit.variables.sample_n_hom_ref_spec": [[106, "sgkit-variables-sample-n-hom-ref-spec"]], "sgkit.variables.sample_n_non_ref_spec": [[107, "sgkit-variables-sample-n-non-ref-spec"]], "sgkit.variables.sample_pca_component_spec": [[108, "sgkit-variables-sample-pca-component-spec"]], "sgkit.variables.sample_pca_explained_variance_ratio_spec": [[109, "sgkit-variables-sample-pca-explained-variance-ratio-spec"]], "sgkit.variables.sample_pca_explained_variance_spec": [[110, "sgkit-variables-sample-pca-explained-variance-spec"]], "sgkit.variables.sample_pca_loading_spec": [[111, "sgkit-variables-sample-pca-loading-spec"]], "sgkit.variables.sample_pca_projection_spec": [[112, "sgkit-variables-sample-pca-projection-spec"]], "sgkit.variables.sample_ploidy_spec": [[113, "sgkit-variables-sample-ploidy-spec"]], "sgkit.variables.stat_Fst_spec": [[114, "sgkit-variables-stat-fst-spec"]], "sgkit.variables.stat_Garud_h123_spec": [[115, "sgkit-variables-stat-garud-h123-spec"]], "sgkit.variables.stat_Garud_h12_spec": [[116, "sgkit-variables-stat-garud-h12-spec"]], "sgkit.variables.stat_Garud_h1_spec": [[117, "sgkit-variables-stat-garud-h1-spec"]], "sgkit.variables.stat_Garud_h2_h1_spec": [[118, "sgkit-variables-stat-garud-h2-h1-spec"]], "sgkit.variables.stat_Hamilton_Kerr_lambda_spec": [[119, "sgkit-variables-stat-hamilton-kerr-lambda-spec"]], "sgkit.variables.stat_Hamilton_Kerr_tau_spec": [[120, "sgkit-variables-stat-hamilton-kerr-tau-spec"]], "sgkit.variables.stat_Tajimas_D_spec": [[121, "sgkit-variables-stat-tajimas-d-spec"]], "sgkit.variables.stat_Weir_Goudet_beta_spec": [[122, "sgkit-variables-stat-weir-goudet-beta-spec"]], "sgkit.variables.stat_divergence_spec": [[123, "sgkit-variables-stat-divergence-spec"]], "sgkit.variables.stat_diversity_spec": [[124, "sgkit-variables-stat-diversity-spec"]], "sgkit.variables.stat_genomic_kinship_spec": [[125, "sgkit-variables-stat-genomic-kinship-spec"]], "sgkit.variables.stat_genomic_relationship_spec": [[126, "sgkit-variables-stat-genomic-relationship-spec"]], "sgkit.variables.stat_hybrid_inverse_relationship_spec": [[127, "sgkit-variables-stat-hybrid-inverse-relationship-spec"]], "sgkit.variables.stat_hybrid_relationship_spec": [[128, "sgkit-variables-stat-hybrid-relationship-spec"]], "sgkit.variables.stat_identity_by_state_spec": [[129, "sgkit-variables-stat-identity-by-state-spec"]], "sgkit.variables.stat_inverse_relationship_spec": [[130, "sgkit-variables-stat-inverse-relationship-spec"]], "sgkit.variables.stat_observed_heterozygosity_spec": [[131, "sgkit-variables-stat-observed-heterozygosity-spec"]], "sgkit.variables.stat_pbs_spec": [[132, "sgkit-variables-stat-pbs-spec"]], "sgkit.variables.stat_pedigree_contribution_spec": [[133, "sgkit-variables-stat-pedigree-contribution-spec"]], "sgkit.variables.stat_pedigree_inbreeding_spec": [[134, "sgkit-variables-stat-pedigree-inbreeding-spec"]], "sgkit.variables.stat_pedigree_inverse_kinship_spec": [[135, "sgkit-variables-stat-pedigree-inverse-kinship-spec"]], "sgkit.variables.stat_pedigree_inverse_relationship_spec": [[136, "sgkit-variables-stat-pedigree-inverse-relationship-spec"]], "sgkit.variables.stat_pedigree_kinship_spec": [[137, "sgkit-variables-stat-pedigree-kinship-spec"]], "sgkit.variables.stat_pedigree_relationship_spec": [[138, "sgkit-variables-stat-pedigree-relationship-spec"]], "sgkit.variables.traits_spec": [[139, "sgkit-variables-traits-spec"]], "sgkit.variables.variant_allele_count_spec": [[140, "sgkit-variables-variant-allele-count-spec"]], "sgkit.variables.variant_allele_frequency_spec": [[141, "sgkit-variables-variant-allele-frequency-spec"]], "sgkit.variables.variant_allele_spec": [[142, "sgkit-variables-variant-allele-spec"]], "sgkit.variables.variant_allele_total_spec": [[143, "sgkit-variables-variant-allele-total-spec"]], "sgkit.variables.variant_call_rate_spec": [[144, "sgkit-variables-variant-call-rate-spec"]], "sgkit.variables.variant_contig_spec": [[145, "sgkit-variables-variant-contig-spec"]], "sgkit.variables.variant_genotype_count_spec": [[146, "sgkit-variables-variant-genotype-count-spec"]], "sgkit.variables.variant_hwe_p_value_spec": [[147, "sgkit-variables-variant-hwe-p-value-spec"]], "sgkit.variables.variant_id_spec": [[148, "sgkit-variables-variant-id-spec"]], "sgkit.variables.variant_linreg_beta_spec": [[149, "sgkit-variables-variant-linreg-beta-spec"]], "sgkit.variables.variant_linreg_p_value_spec": [[150, "sgkit-variables-variant-linreg-p-value-spec"]], "sgkit.variables.variant_linreg_t_value_spec": [[151, "sgkit-variables-variant-linreg-t-value-spec"]], "sgkit.variables.variant_n_called_spec": [[152, "sgkit-variables-variant-n-called-spec"]], "sgkit.variables.variant_n_het_spec": [[153, "sgkit-variables-variant-n-het-spec"]], "sgkit.variables.variant_n_hom_alt_spec": [[154, "sgkit-variables-variant-n-hom-alt-spec"]], "sgkit.variables.variant_n_hom_ref_spec": [[155, "sgkit-variables-variant-n-hom-ref-spec"]], "sgkit.variables.variant_n_non_ref_spec": [[156, "sgkit-variables-variant-n-non-ref-spec"]], "sgkit.variables.variant_ploidy_spec": [[157, "sgkit-variables-variant-ploidy-spec"]], "sgkit.variables.variant_position_spec": [[158, "sgkit-variables-variant-position-spec"]], "sgkit.variables.variant_score_spec": [[159, "sgkit-variables-variant-score-spec"]], "sgkit.variables.window_contig_spec": [[160, "sgkit-variables-window-contig-spec"]], "sgkit.variables.window_start_spec": [[161, "sgkit-variables-window-start-spec"]], "sgkit.variables.window_stop_spec": [[162, "sgkit-variables-window-stop-spec"]], "sgkit.variant_stats": [[163, "sgkit-variant-stats"]], "sgkit.window_by_genome": [[164, "sgkit-window-by-genome"]], "sgkit.window_by_interval": [[165, "sgkit-window-by-interval"]], "sgkit.window_by_position": [[166, "sgkit-window-by-position"]], "sgkit.window_by_variant": [[167, "sgkit-window-by-variant"]], "Getting Started": [[168, "getting-started"]], "Installation": [[168, "installation"], [173, "installation"], [174, "installation"]], "Overview": [[168, "overview"]], "Data structures": [[168, "data-structures"]], "Genetic methods": [[168, "genetic-methods"]], "Missing data": [[168, "missing-data"]], "Windowing": [[168, "windowing"]], "Cohorts": [[168, "cohorts"]], "Chaining operations": [[168, "chaining-operations"]], "Chunked arrays": [[168, "chunked-arrays"]], "How do I \u2026": [[169, "how-do-i"]], "Create a test dataset?": [[169, "create-a-test-dataset"]], "Look at the dataset summary?": [[169, "look-at-the-dataset-summary"]], "Get the values for a variable in a dataset?": [[169, "get-the-values-for-a-variable-in-a-dataset"]], "Find the definition for a variable in a dataset?": [[169, "find-the-definition-for-a-variable-in-a-dataset"]], "Look at the genotypes?": [[169, "look-at-the-genotypes"]], "Subset the variables?": [[169, "subset-the-variables"]], "Subset to a genomic range?": [[169, "subset-to-a-genomic-range"]], "Get the list of samples?": [[169, "get-the-list-of-samples"]], "Subset the samples?": [[169, "subset-the-samples"]], "Define a new variable based on others?": [[169, "define-a-new-variable-based-on-others"]], "Get summary stats?": [[169, "get-summary-stats"]], "Filter variants?": [[169, "filter-variants"]], "Find which new variables were added by a method?": [[169, "find-which-new-variables-were-added-by-a-method"]], "Save results to a Zarr file?": [[169, "save-results-to-a-zarr-file"]], "Load a dataset from Zarr?": [[169, "load-a-dataset-from-zarr"]], "sgkit: Statistical genetics toolkit in Python": [[170, "sgkit-statistical-genetics-toolkit-in-python"]], "Contents": [[170, null]], "Indices and tables": [[170, "indices-and-tables"]], "News": [[171, "news"]], "Introducing sgkit": [[172, "introducing-sgkit"]], "User Guide": [[173, "user-guide"]], "Reading and writing genetic data": [[173, "reading-and-writing-genetic-data"]], "Converting genetic data to Zarr": [[173, "converting-genetic-data-to-zarr"]], "VCF": [[173, "vcf"]], "Working with cloud-native data": [[173, "working-with-cloud-native-data"]], "Datasets": [[173, "datasets"]], "Genetic variables": [[173, "genetic-variables"]], "Dataset merge behavior": [[173, "dataset-merge-behavior"]], "Interop with other Python libraries": [[173, "interop-with-other-python-libraries"]], "Custom naming conventions": [[173, "custom-naming-conventions"]], "Adding custom data to a Dataset": [[173, "adding-custom-data-to-a-dataset"]], "Custom Computations": [[173, "custom-computations"]], "PCA": [[173, "pca"]], "Deployment": [[173, "deployment"]], "Deploying sgkit on a cluster": [[173, "deploying-sgkit-on-a-cluster"]], "Using GPUs": [[173, "using-gpus"]], "Troubleshooting": [[173, "troubleshooting"]], "Monitoring operations": [[173, "monitoring-operations"]], "Visualizing computations": [[173, "visualizing-computations"]], "Disabling the Numba cache": [[173, "disabling-the-numba-cache"]], "Reading VCF": [[174, "reading-vcf"]], "Highlights": [[174, "highlights"]], "Usage": [[174, "usage"]], "Multiple files": [[174, "multiple-files"]], "Partitioning": [[174, "partitioning"]], "Chunk sizes": [[174, "chunk-sizes"]], "Cloud storage": [[174, "cloud-storage"]], "Compression": [[174, "compression"]], "Low-level operation": [[174, "low-level-operation"]], "Polyploid and mixed-ploidy VCF": [[174, "polyploid-and-mixed-ploidy-vcf"]], "Example: converting 1000 genomes VCF to Zarr": [[174, "example-converting-1000-genomes-vcf-to-zarr"]], "Install sgkit": [[174, "install-sgkit"]], "Download the data": [[174, "download-the-data"]], "Run the conversion": [[174, "run-the-conversion"]], "Inspect the dataset": [[174, "inspect-the-dataset"]]}, "indexentries": {"fst() (in module sgkit)": [[7, "sgkit.Fst"]], "garud_h() (in module sgkit)": [[8, "sgkit.Garud_H"]], "tajimas_d() (in module sgkit)": [[9, "sgkit.Tajimas_D"]], "weir_goudet_beta() (in module sgkit)": [[10, "sgkit.Weir_Goudet_beta"]], "call_allele_frequencies() (in module sgkit)": [[11, "sgkit.call_allele_frequencies"]], "cohort_allele_frequencies() (in module sgkit)": [[12, "sgkit.cohort_allele_frequencies"]], "convert_call_to_index() (in module sgkit)": [[13, "sgkit.convert_call_to_index"]], "convert_probability_to_call() (in module sgkit)": [[14, "sgkit.convert_probability_to_call"]], "count_call_alleles() (in module sgkit)": [[15, "sgkit.count_call_alleles"]], "count_cohort_alleles() (in module sgkit)": [[16, "sgkit.count_cohort_alleles"]], "count_variant_alleles() (in module sgkit)": [[17, "sgkit.count_variant_alleles"]], "count_variant_genotypes() (in module sgkit)": [[18, "sgkit.count_variant_genotypes"]], "display_genotypes() (in module sgkit)": [[19, "sgkit.display_genotypes"]], "display_pedigree() (in module sgkit)": [[20, "sgkit.display_pedigree"]], "divergence() (in module sgkit)": [[21, "sgkit.divergence"]], "diversity() (in module sgkit)": [[22, "sgkit.diversity"]], "filter_partial_calls() (in module sgkit)": [[23, "sgkit.filter_partial_calls"]], "genee() (in module sgkit)": [[24, "sgkit.genee"]], "genomic_relationship() (in module sgkit)": [[25, "sgkit.genomic_relationship"]], "gwas_linear_regression() (in module sgkit)": [[26, "sgkit.gwas_linear_regression"]], "hardy_weinberg_test() (in module sgkit)": [[27, "sgkit.hardy_weinberg_test"]], "hybrid_inverse_relationship() (in module sgkit)": [[28, "sgkit.hybrid_inverse_relationship"]], "hybrid_relationship() (in module sgkit)": [[29, "sgkit.hybrid_relationship"]], "identity_by_state() (in module sgkit)": [[30, "sgkit.identity_by_state"]], "individual_heterozygosity() (in module sgkit)": [[31, "sgkit.individual_heterozygosity"]], "infer_call_ploidy() (in module sgkit)": [[32, "sgkit.infer_call_ploidy"]], "infer_sample_ploidy() (in module sgkit)": [[33, "sgkit.infer_sample_ploidy"]], "infer_variant_ploidy() (in module sgkit)": [[34, "sgkit.infer_variant_ploidy"]], "invert_relationship_matrix() (in module sgkit)": [[35, "sgkit.invert_relationship_matrix"]], "bgen_to_zarr() (in module sgkit.io.bgen)": [[36, "sgkit.io.bgen.bgen_to_zarr"]], "read_bgen() (in module sgkit.io.bgen)": [[37, "sgkit.io.bgen.read_bgen"]], "rechunk_bgen() (in module sgkit.io.bgen)": [[38, "sgkit.io.bgen.rechunk_bgen"]], "plink_to_zarr() (in module sgkit.io.plink)": [[39, "sgkit.io.plink.plink_to_zarr"]], "read_plink() (in module sgkit.io.plink)": [[40, "sgkit.io.plink.read_plink"]], "write_plink() (in module sgkit.io.plink)": [[41, "sgkit.io.plink.write_plink"]], "zarr_to_plink() (in module sgkit.io.plink)": [[42, "sgkit.io.plink.zarr_to_plink"]], "concat_zarrs() (in module sgkit.io.vcf)": [[43, "sgkit.io.vcf.concat_zarrs"]], "partition_into_regions() (in module sgkit.io.vcf)": [[44, "sgkit.io.vcf.partition_into_regions"]], "read_vcf() (in module sgkit.io.vcf)": [[45, "sgkit.io.vcf.read_vcf"]], "vcf_to_zarr() (in module sgkit.io.vcf)": [[46, "sgkit.io.vcf.vcf_to_zarr"]], "vcf_to_zarrs() (in module sgkit.io.vcf)": [[47, "sgkit.io.vcf.vcf_to_zarrs"]], "write_vcf() (in module sgkit.io.vcf)": [[48, "sgkit.io.vcf.write_vcf"]], "zarr_array_sizes() (in module sgkit.io.vcf)": [[49, "sgkit.io.vcf.zarr_array_sizes"]], "zarr_to_vcf() (in module sgkit.io.vcf)": [[50, "sgkit.io.vcf.zarr_to_vcf"]], "ld_matrix() (in module sgkit)": [[51, "sgkit.ld_matrix"]], "ld_prune() (in module sgkit)": [[52, "sgkit.ld_prune"]], "load_dataset() (in module sgkit)": [[53, "sgkit.load_dataset"]], "maximal_independent_set() (in module sgkit)": [[54, "sgkit.maximal_independent_set"]], "observed_heterozygosity() (in module sgkit)": [[55, "sgkit.observed_heterozygosity"]], "pairwise_distance() (in module sgkit)": [[56, "sgkit.pairwise_distance"]], "parent_indices() (in module sgkit)": [[57, "sgkit.parent_indices"]], "pbs() (in module sgkit)": [[58, "sgkit.pbs"]], "pc_relate() (in module sgkit)": [[59, "sgkit.pc_relate"]], "pedigree_contribution() (in module sgkit)": [[60, "sgkit.pedigree_contribution"]], "pedigree_inbreeding() (in module sgkit)": [[61, "sgkit.pedigree_inbreeding"]], "pedigree_inverse_kinship() (in module sgkit)": [[62, "sgkit.pedigree_inverse_kinship"]], "pedigree_kinship() (in module sgkit)": [[63, "sgkit.pedigree_kinship"]], "pedigree_sel() (in module sgkit)": [[64, "sgkit.pedigree_sel"]], "read_scikit_allel_vcfzarr() (in module sgkit)": [[65, "sgkit.read_scikit_allel_vcfzarr"]], "regenie() (in module sgkit)": [[66, "sgkit.regenie"]], "sample_stats() (in module sgkit)": [[67, "sgkit.sample_stats"]], "save_dataset() (in module sgkit)": [[68, "sgkit.save_dataset"]], "simulate_genedrop() (in module sgkit)": [[69, "sgkit.simulate_genedrop"]], "simulate_genotype_call_dataset() (in module sgkit)": [[70, "sgkit.simulate_genotype_call_dataset"]], "call_allele_count_spec (in module sgkit.variables)": [[71, "sgkit.variables.call_allele_count_spec"]], "call_allele_frequency_spec (in module sgkit.variables)": [[72, "sgkit.variables.call_allele_frequency_spec"]], "call_dosage_mask_spec (in module sgkit.variables)": [[73, "sgkit.variables.call_dosage_mask_spec"]], "call_dosage_spec (in module sgkit.variables)": [[74, "sgkit.variables.call_dosage_spec"]], "call_genotype_complete_mask_spec (in module sgkit.variables)": [[75, "sgkit.variables.call_genotype_complete_mask_spec"]], "call_genotype_complete_spec (in module sgkit.variables)": [[76, "sgkit.variables.call_genotype_complete_spec"]], "call_genotype_fill_spec (in module sgkit.variables)": [[77, "sgkit.variables.call_genotype_fill_spec"]], "call_genotype_index_mask_spec (in module sgkit.variables)": [[78, "sgkit.variables.call_genotype_index_mask_spec"]], "call_genotype_index_spec (in module sgkit.variables)": [[79, "sgkit.variables.call_genotype_index_spec"]], "call_genotype_mask_spec (in module sgkit.variables)": [[80, "sgkit.variables.call_genotype_mask_spec"]], "call_genotype_phased_spec (in module sgkit.variables)": [[81, "sgkit.variables.call_genotype_phased_spec"]], "call_genotype_probability_mask_spec (in module sgkit.variables)": [[82, "sgkit.variables.call_genotype_probability_mask_spec"]], "call_genotype_probability_spec (in module sgkit.variables)": [[83, "sgkit.variables.call_genotype_probability_spec"]], "call_genotype_spec (in module sgkit.variables)": [[84, "sgkit.variables.call_genotype_spec"]], "call_heterozygosity_spec (in module sgkit.variables)": [[85, "sgkit.variables.call_heterozygosity_spec"]], "call_ploidy_spec (in module sgkit.variables)": [[86, "sgkit.variables.call_ploidy_spec"]], "cohort_allele_count_spec (in module sgkit.variables)": [[87, "sgkit.variables.cohort_allele_count_spec"]], "cohort_allele_frequency_spec (in module sgkit.variables)": [[88, "sgkit.variables.cohort_allele_frequency_spec"]], "covariates_spec (in module sgkit.variables)": [[89, "sgkit.variables.covariates_spec"]], "interval_contig_name_spec (in module sgkit.variables)": [[90, "sgkit.variables.interval_contig_name_spec"]], "interval_start_spec (in module sgkit.variables)": [[91, "sgkit.variables.interval_start_spec"]], "interval_stop_spec (in module sgkit.variables)": [[92, "sgkit.variables.interval_stop_spec"]], "ld_prune_index_to_drop_spec (in module sgkit.variables)": [[93, "sgkit.variables.ld_prune_index_to_drop_spec"]], "parent_id_spec (in module sgkit.variables)": [[94, "sgkit.variables.parent_id_spec"]], "parent_spec (in module sgkit.variables)": [[95, "sgkit.variables.parent_spec"]], "pc_relate_phi_spec (in module sgkit.variables)": [[96, "sgkit.variables.pc_relate_phi_spec"]], "regenie_base_prediction_spec (in module sgkit.variables)": 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sgkit.variables)": [[151, "sgkit.variables.variant_linreg_t_value_spec"]], "variant_n_called_spec (in module sgkit.variables)": [[152, "sgkit.variables.variant_n_called_spec"]], "variant_n_het_spec (in module sgkit.variables)": [[153, "sgkit.variables.variant_n_het_spec"]], "variant_n_hom_alt_spec (in module sgkit.variables)": [[154, "sgkit.variables.variant_n_hom_alt_spec"]], "variant_n_hom_ref_spec (in module sgkit.variables)": [[155, "sgkit.variables.variant_n_hom_ref_spec"]], "variant_n_non_ref_spec (in module sgkit.variables)": [[156, "sgkit.variables.variant_n_non_ref_spec"]], "variant_ploidy_spec (in module sgkit.variables)": [[157, "sgkit.variables.variant_ploidy_spec"]], "variant_position_spec (in module sgkit.variables)": [[158, "sgkit.variables.variant_position_spec"]], "variant_score_spec (in module sgkit.variables)": [[159, "sgkit.variables.variant_score_spec"]], "window_contig_spec (in module sgkit.variables)": [[160, "sgkit.variables.window_contig_spec"]], 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4, 6, 14, 19, 24, 28, 29, 32, 36, 37, 44, 45, 46, 47, 48, 59, 61, 62, 63, 65, 69, 173, 174], "similarli": [2, 173], "integ": [2, 4, 6, 13, 36, 37, 39, 40, 44, 45, 46, 47, 57, 63, 64, 65, 69, 79, 145, 168, 169, 173, 174], "int": [2, 8, 19, 25, 27, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 49, 56, 58, 64, 66, 70, 166, 167, 174], "jeromekelleh": 2, "1190": 2, "1192": 2, "max_str_len": 2, "util": [2, 4, 28, 29, 168, 170, 173], "return": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "python": [2, 4, 6, 48, 165, 168, 174], "arrai": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 37, 39, 40, 45, 46, 47, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66, 69, 79, 89, 112, 139, 166, 167, 169, 170, 173, 174], "scalar": [2, 168], "1086": 2, "1085": 2, "turn": 2, "off": [2, 168, 174], "numba": [2, 48], "cach": 2, "default": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "1191": 2, "1156": 2, "xarrai": [2, 3, 4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 28, 29, 35, 45, 46, 47, 53, 55, 58, 66, 68, 70, 164, 166, 167, 168, 169, 170, 172, 173, 174], "repr": [2, 169], "doctest": [2, 3], "1205": 2, "1204": 2, "avoid": [2, 3, 4, 6, 35, 45, 46, 51, 52, 168, 169, 174], "disabl": [2, 14], "jit": [2, 173], "guvectoris": 2, "1199": 2, "1194": 2, "relationship": [2, 25, 28, 29, 35, 59, 61, 62, 63, 69, 126, 127, 128, 130, 136, 138], "matric": [2, 28, 29], "1072": 2, "956": 2, "pairwise_dist": 2, "doc": [2, 3, 37, 39, 40], "benjefferi": 2, "1145": 2, "1142": 2, "format": [2, 3, 4, 6, 19, 40, 45, 46, 47, 65, 168, 171, 172, 173, 174], "matrix": [2, 6, 10, 25, 28, 29, 30, 35, 51, 52, 54, 56, 59, 61, 62, 63, 69, 96, 108, 110, 125, 126, 127, 128, 130, 133, 135, 136, 138, 159], "pairwis": [2, 6, 10, 25, 28, 29, 30, 56, 59, 63, 122, 129, 137], "1148": 2, "1147": 2, "io": [2, 3, 6, 14, 65, 66, 170, 173, 174], "plink": [2, 6, 54, 168, 172], "write_plink": [2, 42, 173], "1003": 2, "926": [2, 168], "phase": [2, 19, 36, 65, 70, 81], "simulate_genotype_call_dataset": [2, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 52, 55, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 173], "1022": 2, "973": 2, "plink_to_zarr": 2, "zarr_to_plink": [2, 173], "conveni": [2, 4, 26, 36, 39, 42, 45, 50, 70, 168, 173], "1047": 2, "1004": 2, "convert_call_to_index": [2, 173], "1050": 2, "1048": 2, "read_chunk_length": [2, 46, 47], "vcf_to_zarr": [2, 43, 45, 48, 65, 173, 174], "These": [2, 3, 6, 25, 27, 66, 110, 111, 168, 173], "reduc": [2, 46, 47, 56, 168], "memori": [2, 4, 36, 37, 38, 39, 40, 45, 46, 47, 48, 54, 61, 168, 169, 173, 174], "usag": [2, 4, 46, 47, 61, 168, 170], "larg": [2, 3, 26, 30, 45, 46, 47, 51, 52, 168, 170, 173, 174], "sampl": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 45, 46, 47, 48, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 89, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 112, 113, 119, 120, 122, 129, 133, 134, 137, 139, 144, 152, 153, 154, 155, 156, 157, 163, 168, 170, 172, 173, 174], "chunk_length": [2, 36, 38, 43, 45, 46, 47, 174], "1044": 2, "1042": 2, "retain_temp_fil": [2, 46], "1046": 2, "1036": 2, "read_vcf": 2, "1052": 2, "hybrid_relationship": [2, 6, 28], "hybrid_inverse_relationship": [2, 29], "invert_relationship_matrix": [2, 6, 28, 29], "1053": 2, "993": [2, 6], "zarr_array_s": 2, "determin": [2, 3, 7, 37, 49, 56, 168], "size": [2, 4, 6, 7, 8, 9, 12, 16, 18, 21, 22, 24, 25, 26, 35, 37, 39, 40, 44, 45, 46, 47, 48, 49, 52, 55, 56, 58, 63, 66, 79, 164, 166, 167, 168, 169, 170, 173], "storag": [2, 4, 6, 39, 43, 44, 45, 46, 47, 49, 53, 68, 168, 170, 173], "1073": 2, "734": 2, "skipna": [2, 25, 30], "1078": 2, "1076": 2, "additional_variant_field": [2, 70], "1056": 2, "header": [2, 45, 46, 47, 48, 50, 65], "when": [2, 3, 6, 17, 26, 28, 29, 30, 36, 37, 38, 39, 40, 45, 46, 47, 55, 63, 67, 69, 70, 120, 159, 163, 168, 173, 174], "write": [2, 3, 4, 6, 46, 48, 170, 172, 174], "write_vcf": [2, 50, 173], "zarr_to_vcf": [2, 48, 173], "previous": [2, 3], "dataset": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 84, 89, 120, 139, 163, 164, 165, 166, 167, 168, 170], "had": [2, 6], "contain": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 39, 40, 41, 47, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 98, 130, 139, 163, 164, 165, 166, 167, 168, 173], "vcf_header": [2, 48, 50], "attribut": [2, 4, 6, 20, 48, 50, 90, 168, 169, 173, 174], "1021": 2, "1020": 2, "contig": [2, 4, 37, 39, 40, 66, 70, 90, 98, 145, 160, 165, 166, 167, 168, 169, 173, 174], "contig_id": [2, 4, 168, 169], "filter": [2, 4, 6, 45, 46, 47, 59, 168, 170, 174], "filter_id": [2, 4], "duplic": [2, 3, 69], "inform": [2, 3, 4, 6, 7, 9, 19, 21, 22, 28, 29, 37, 39, 40, 45, 46, 47, 52, 58, 65, 165, 166, 167, 168, 173, 174], "which": [2, 3, 4, 6, 10, 21, 23, 25, 27, 28, 29, 30, 35, 36, 38, 41, 44, 45, 46, 47, 49, 51, 52, 56, 61, 62, 63, 65, 66, 69, 73, 75, 76, 78, 80, 82, 120, 130, 133, 166, 168, 170, 171, 172, 173, 174], "now": [2, 3, 4, 6, 56, 168, 172, 173], "remov": [2, 4, 6, 23, 25, 26, 36, 38, 52, 57, 66, 169], "futur": [2, 3, 6, 172, 173], "releas": [2, 3, 4, 6, 171, 172, 174], "1054": 2, "1035": 2, "paramet": [2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 173, 174], "founder_indic": [2, 63], "pedigree_kinship": [2, 6], "instead": [2, 6, 36, 38, 63], "founder_kinship": [2, 63], "expect": [2, 4, 6, 60, 61, 63, 133, 134, 137, 173, 174], "full": [2, 4, 6, 28, 29, 39, 40, 41, 42, 59, 61, 63, 168, 173, 174], "kinship": [2, 6, 10, 59, 61, 62, 63, 96, 125, 135, 137, 172], "founder": [2, 6, 61, 62, 63, 69], "ignor": [2, 4, 6, 29, 45, 46, 48, 49, 55, 56, 63, 66, 67, 98, 163, 168], "1075": 2, "1061": 2, "scale": [2, 4, 6, 10, 28, 29, 111, 168, 170, 173, 174], "number": [2, 3, 4, 6, 15, 16, 17, 18, 19, 25, 27, 32, 33, 34, 36, 38, 41, 44, 45, 46, 47, 59, 63, 65, 66, 67, 69, 70, 71, 103, 104, 105, 106, 107, 120, 140, 143, 146, 152, 153, 154, 155, 156, 163, 166, 167, 168, 173, 174], "1028": 2, "1026": 2, "1027": 2, "import": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 28, 29, 30, 31, 35, 37, 39, 40, 48, 52, 55, 56, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 170, 173, 174], "much": [2, 4, 6, 36, 37, 38, 174], "faster": [2, 4, 63, 173, 174], "due": [2, 3, 6, 60, 168, 174], "defer": 2, "compil": [2, 168, 173], "1039": [2, 3], "939": 2, "wa": [2, 3, 4, 25, 35, 38, 172], "output": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 43, 45, 46, 47, 48, 50, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 173, 174], "file": [2, 3, 4, 6, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 65, 68, 170, 172, 173], "temp_chunk_length": [2, 36, 45, 46, 174], "chunk": [2, 4, 6, 7, 9, 21, 22, 35, 36, 37, 38, 39, 40, 43, 45, 46, 47, 48, 58, 60, 68, 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"sgkit-sample-stats"]], "sgkit.save_dataset": [[68, "sgkit-save-dataset"]], "sgkit.simulate_genedrop": [[69, "sgkit-simulate-genedrop"]], "sgkit.simulate_genotype_call_dataset": [[70, "sgkit-simulate-genotype-call-dataset"]], "sgkit.variables.call_allele_count_spec": [[71, "sgkit-variables-call-allele-count-spec"]], "sgkit.variables.call_allele_frequency_spec": [[72, "sgkit-variables-call-allele-frequency-spec"]], "sgkit.variables.call_dosage_mask_spec": [[73, "sgkit-variables-call-dosage-mask-spec"]], "sgkit.variables.call_dosage_spec": [[74, "sgkit-variables-call-dosage-spec"]], "sgkit.variables.call_genotype_complete_mask_spec": [[75, "sgkit-variables-call-genotype-complete-mask-spec"]], "sgkit.variables.call_genotype_complete_spec": [[76, "sgkit-variables-call-genotype-complete-spec"]], "sgkit.variables.call_genotype_fill_spec": [[77, "sgkit-variables-call-genotype-fill-spec"]], "sgkit.variables.call_genotype_index_mask_spec": [[78, "sgkit-variables-call-genotype-index-mask-spec"]], "sgkit.variables.call_genotype_index_spec": [[79, "sgkit-variables-call-genotype-index-spec"]], "sgkit.variables.call_genotype_mask_spec": [[80, "sgkit-variables-call-genotype-mask-spec"]], "sgkit.variables.call_genotype_phased_spec": [[81, "sgkit-variables-call-genotype-phased-spec"]], "sgkit.variables.call_genotype_probability_mask_spec": [[82, "sgkit-variables-call-genotype-probability-mask-spec"]], "sgkit.variables.call_genotype_probability_spec": [[83, "sgkit-variables-call-genotype-probability-spec"]], "sgkit.variables.call_genotype_spec": [[84, "sgkit-variables-call-genotype-spec"]], "sgkit.variables.call_heterozygosity_spec": [[85, "sgkit-variables-call-heterozygosity-spec"]], "sgkit.variables.call_ploidy_spec": [[86, "sgkit-variables-call-ploidy-spec"]], "sgkit.variables.cohort_allele_count_spec": [[87, "sgkit-variables-cohort-allele-count-spec"]], "sgkit.variables.cohort_allele_frequency_spec": [[88, "sgkit-variables-cohort-allele-frequency-spec"]], "sgkit.variables.covariates_spec": [[89, "sgkit-variables-covariates-spec"]], "sgkit.variables.interval_contig_name_spec": [[90, "sgkit-variables-interval-contig-name-spec"]], "sgkit.variables.interval_start_spec": [[91, "sgkit-variables-interval-start-spec"]], "sgkit.variables.interval_stop_spec": [[92, "sgkit-variables-interval-stop-spec"]], "sgkit.variables.ld_prune_index_to_drop_spec": [[93, "sgkit-variables-ld-prune-index-to-drop-spec"]], "sgkit.variables.parent_id_spec": [[94, "sgkit-variables-parent-id-spec"]], "sgkit.variables.parent_spec": [[95, "sgkit-variables-parent-spec"]], "sgkit.variables.pc_relate_phi_spec": [[96, "sgkit-variables-pc-relate-phi-spec"]], "sgkit.variables.regenie_base_prediction_spec": [[97, "sgkit-variables-regenie-base-prediction-spec"]], "sgkit.variables.regenie_loco_prediction_spec": [[98, "sgkit-variables-regenie-loco-prediction-spec"]], "sgkit.variables.regenie_meta_prediction_spec": [[99, "sgkit-variables-regenie-meta-prediction-spec"]], "sgkit.variables.sample_call_rate_spec": [[100, "sgkit-variables-sample-call-rate-spec"]], "sgkit.variables.sample_cohort_spec": [[101, "sgkit-variables-sample-cohort-spec"]], "sgkit.variables.sample_id_spec": [[102, "sgkit-variables-sample-id-spec"]], "sgkit.variables.sample_n_called_spec": [[103, "sgkit-variables-sample-n-called-spec"]], "sgkit.variables.sample_n_het_spec": [[104, "sgkit-variables-sample-n-het-spec"]], "sgkit.variables.sample_n_hom_alt_spec": [[105, "sgkit-variables-sample-n-hom-alt-spec"]], "sgkit.variables.sample_n_hom_ref_spec": [[106, "sgkit-variables-sample-n-hom-ref-spec"]], "sgkit.variables.sample_n_non_ref_spec": [[107, "sgkit-variables-sample-n-non-ref-spec"]], "sgkit.variables.sample_pca_component_spec": [[108, "sgkit-variables-sample-pca-component-spec"]], "sgkit.variables.sample_pca_explained_variance_ratio_spec": [[109, "sgkit-variables-sample-pca-explained-variance-ratio-spec"]], "sgkit.variables.sample_pca_explained_variance_spec": [[110, "sgkit-variables-sample-pca-explained-variance-spec"]], "sgkit.variables.sample_pca_loading_spec": [[111, "sgkit-variables-sample-pca-loading-spec"]], "sgkit.variables.sample_pca_projection_spec": [[112, "sgkit-variables-sample-pca-projection-spec"]], "sgkit.variables.sample_ploidy_spec": [[113, "sgkit-variables-sample-ploidy-spec"]], "sgkit.variables.stat_Fst_spec": [[114, "sgkit-variables-stat-fst-spec"]], "sgkit.variables.stat_Garud_h123_spec": [[115, "sgkit-variables-stat-garud-h123-spec"]], "sgkit.variables.stat_Garud_h12_spec": [[116, "sgkit-variables-stat-garud-h12-spec"]], "sgkit.variables.stat_Garud_h1_spec": [[117, "sgkit-variables-stat-garud-h1-spec"]], "sgkit.variables.stat_Garud_h2_h1_spec": [[118, "sgkit-variables-stat-garud-h2-h1-spec"]], "sgkit.variables.stat_Hamilton_Kerr_lambda_spec": [[119, "sgkit-variables-stat-hamilton-kerr-lambda-spec"]], "sgkit.variables.stat_Hamilton_Kerr_tau_spec": [[120, "sgkit-variables-stat-hamilton-kerr-tau-spec"]], "sgkit.variables.stat_Tajimas_D_spec": [[121, "sgkit-variables-stat-tajimas-d-spec"]], "sgkit.variables.stat_Weir_Goudet_beta_spec": [[122, "sgkit-variables-stat-weir-goudet-beta-spec"]], "sgkit.variables.stat_divergence_spec": [[123, "sgkit-variables-stat-divergence-spec"]], "sgkit.variables.stat_diversity_spec": [[124, "sgkit-variables-stat-diversity-spec"]], "sgkit.variables.stat_genomic_kinship_spec": [[125, "sgkit-variables-stat-genomic-kinship-spec"]], "sgkit.variables.stat_genomic_relationship_spec": [[126, "sgkit-variables-stat-genomic-relationship-spec"]], "sgkit.variables.stat_hybrid_inverse_relationship_spec": [[127, "sgkit-variables-stat-hybrid-inverse-relationship-spec"]], "sgkit.variables.stat_hybrid_relationship_spec": [[128, "sgkit-variables-stat-hybrid-relationship-spec"]], "sgkit.variables.stat_identity_by_state_spec": [[129, "sgkit-variables-stat-identity-by-state-spec"]], "sgkit.variables.stat_inverse_relationship_spec": [[130, "sgkit-variables-stat-inverse-relationship-spec"]], "sgkit.variables.stat_observed_heterozygosity_spec": [[131, "sgkit-variables-stat-observed-heterozygosity-spec"]], "sgkit.variables.stat_pbs_spec": [[132, "sgkit-variables-stat-pbs-spec"]], "sgkit.variables.stat_pedigree_contribution_spec": [[133, "sgkit-variables-stat-pedigree-contribution-spec"]], "sgkit.variables.stat_pedigree_inbreeding_spec": [[134, "sgkit-variables-stat-pedigree-inbreeding-spec"]], "sgkit.variables.stat_pedigree_inverse_kinship_spec": [[135, "sgkit-variables-stat-pedigree-inverse-kinship-spec"]], "sgkit.variables.stat_pedigree_inverse_relationship_spec": [[136, "sgkit-variables-stat-pedigree-inverse-relationship-spec"]], "sgkit.variables.stat_pedigree_kinship_spec": [[137, "sgkit-variables-stat-pedigree-kinship-spec"]], "sgkit.variables.stat_pedigree_relationship_spec": [[138, "sgkit-variables-stat-pedigree-relationship-spec"]], "sgkit.variables.traits_spec": [[139, "sgkit-variables-traits-spec"]], "sgkit.variables.variant_allele_count_spec": [[140, "sgkit-variables-variant-allele-count-spec"]], "sgkit.variables.variant_allele_frequency_spec": [[141, "sgkit-variables-variant-allele-frequency-spec"]], "sgkit.variables.variant_allele_spec": [[142, "sgkit-variables-variant-allele-spec"]], "sgkit.variables.variant_allele_total_spec": [[143, "sgkit-variables-variant-allele-total-spec"]], "sgkit.variables.variant_call_rate_spec": [[144, "sgkit-variables-variant-call-rate-spec"]], "sgkit.variables.variant_contig_spec": [[145, "sgkit-variables-variant-contig-spec"]], "sgkit.variables.variant_genotype_count_spec": [[146, "sgkit-variables-variant-genotype-count-spec"]], "sgkit.variables.variant_hwe_p_value_spec": [[147, "sgkit-variables-variant-hwe-p-value-spec"]], "sgkit.variables.variant_id_spec": [[148, "sgkit-variables-variant-id-spec"]], "sgkit.variables.variant_linreg_beta_spec": [[149, "sgkit-variables-variant-linreg-beta-spec"]], "sgkit.variables.variant_linreg_p_value_spec": [[150, "sgkit-variables-variant-linreg-p-value-spec"]], "sgkit.variables.variant_linreg_t_value_spec": [[151, "sgkit-variables-variant-linreg-t-value-spec"]], "sgkit.variables.variant_n_called_spec": [[152, "sgkit-variables-variant-n-called-spec"]], "sgkit.variables.variant_n_het_spec": [[153, "sgkit-variables-variant-n-het-spec"]], "sgkit.variables.variant_n_hom_alt_spec": [[154, "sgkit-variables-variant-n-hom-alt-spec"]], "sgkit.variables.variant_n_hom_ref_spec": [[155, "sgkit-variables-variant-n-hom-ref-spec"]], "sgkit.variables.variant_n_non_ref_spec": [[156, "sgkit-variables-variant-n-non-ref-spec"]], "sgkit.variables.variant_ploidy_spec": [[157, "sgkit-variables-variant-ploidy-spec"]], "sgkit.variables.variant_position_spec": [[158, "sgkit-variables-variant-position-spec"]], "sgkit.variables.variant_score_spec": [[159, "sgkit-variables-variant-score-spec"]], "sgkit.variables.window_contig_spec": [[160, "sgkit-variables-window-contig-spec"]], "sgkit.variables.window_start_spec": [[161, "sgkit-variables-window-start-spec"]], "sgkit.variables.window_stop_spec": [[162, "sgkit-variables-window-stop-spec"]], "sgkit.variant_stats": [[163, "sgkit-variant-stats"]], "sgkit.window_by_genome": [[164, "sgkit-window-by-genome"]], "sgkit.window_by_interval": [[165, "sgkit-window-by-interval"]], "sgkit.window_by_position": [[166, "sgkit-window-by-position"]], "sgkit.window_by_variant": [[167, "sgkit-window-by-variant"]], "Getting Started": [[168, "getting-started"]], "Installation": [[168, "installation"], [173, "installation"], [174, "installation"]], "Overview": [[168, "overview"]], "Data structures": [[168, "data-structures"]], "Genetic methods": [[168, "genetic-methods"]], "Missing data": [[168, "missing-data"]], "Windowing": [[168, "windowing"]], "Cohorts": [[168, "cohorts"]], "Chaining operations": [[168, "chaining-operations"]], "Chunked arrays": [[168, "chunked-arrays"]], "How do I \u2026": [[169, "how-do-i"]], "Create a test dataset?": [[169, "create-a-test-dataset"]], "Look at the dataset summary?": [[169, "look-at-the-dataset-summary"]], "Get the values for a variable in a dataset?": [[169, "get-the-values-for-a-variable-in-a-dataset"]], "Find the definition for a variable in a dataset?": [[169, "find-the-definition-for-a-variable-in-a-dataset"]], "Look at the genotypes?": [[169, "look-at-the-genotypes"]], "Subset the variables?": [[169, "subset-the-variables"]], "Subset to a genomic range?": [[169, "subset-to-a-genomic-range"]], "Get the list of samples?": [[169, "get-the-list-of-samples"]], "Subset the samples?": [[169, "subset-the-samples"]], "Define a new variable based on others?": [[169, "define-a-new-variable-based-on-others"]], "Get summary stats?": [[169, "get-summary-stats"]], "Filter variants?": [[169, "filter-variants"]], "Find which new variables were added by a method?": [[169, "find-which-new-variables-were-added-by-a-method"]], "Save results to a Zarr file?": [[169, "save-results-to-a-zarr-file"]], "Load a dataset from Zarr?": [[169, "load-a-dataset-from-zarr"]], "sgkit: Statistical genetics toolkit in Python": [[170, "sgkit-statistical-genetics-toolkit-in-python"]], "Contents": [[170, null]], "Indices and tables": [[170, "indices-and-tables"]], "News": [[171, "news"]], "Introducing sgkit": [[172, "introducing-sgkit"]], "User Guide": [[173, "user-guide"]], "Reading and writing genetic data": [[173, "reading-and-writing-genetic-data"]], "Converting genetic data to Zarr": [[173, "converting-genetic-data-to-zarr"]], "VCF": [[173, "vcf"]], "Working with cloud-native data": [[173, "working-with-cloud-native-data"]], "Datasets": [[173, "datasets"]], "Genetic variables": [[173, "genetic-variables"]], "Dataset merge behavior": [[173, "dataset-merge-behavior"]], "Interop with other Python libraries": [[173, "interop-with-other-python-libraries"]], "Custom naming conventions": [[173, "custom-naming-conventions"]], "Adding custom data to a Dataset": [[173, "adding-custom-data-to-a-dataset"]], "Custom Computations": [[173, "custom-computations"]], "PCA": [[173, "pca"]], "Deployment": [[173, "deployment"]], "Deploying sgkit on a cluster": [[173, "deploying-sgkit-on-a-cluster"]], "Using GPUs": [[173, "using-gpus"]], "Troubleshooting": [[173, "troubleshooting"]], "Monitoring operations": [[173, "monitoring-operations"]], "Visualizing computations": [[173, "visualizing-computations"]], "Disabling the Numba cache": [[173, "disabling-the-numba-cache"]], "Reading VCF": [[174, "reading-vcf"]], "Highlights": [[174, "highlights"]], "Usage": [[174, "usage"]], "Multiple files": [[174, "multiple-files"]], "Partitioning": [[174, "partitioning"]], "Chunk sizes": [[174, "chunk-sizes"]], "Cloud storage": [[174, "cloud-storage"]], "Compression": [[174, "compression"]], "Low-level operation": [[174, "low-level-operation"]], "Polyploid and mixed-ploidy VCF": [[174, "polyploid-and-mixed-ploidy-vcf"]], "Example: converting 1000 genomes VCF to Zarr": [[174, "example-converting-1000-genomes-vcf-to-zarr"]], "Install sgkit": [[174, "install-sgkit"]], "Download the data": [[174, "download-the-data"]], "Run the conversion": [[174, "run-the-conversion"]], "Inspect the dataset": [[174, "inspect-the-dataset"]]}, "indexentries": {"fst() (in module sgkit)": [[7, "sgkit.Fst"]], "garud_h() (in module sgkit)": [[8, "sgkit.Garud_H"]], "tajimas_d() (in module sgkit)": [[9, "sgkit.Tajimas_D"]], "weir_goudet_beta() (in module sgkit)": [[10, "sgkit.Weir_Goudet_beta"]], "call_allele_frequencies() (in module sgkit)": [[11, "sgkit.call_allele_frequencies"]], "cohort_allele_frequencies() (in module sgkit)": [[12, "sgkit.cohort_allele_frequencies"]], "convert_call_to_index() (in module sgkit)": [[13, "sgkit.convert_call_to_index"]], "convert_probability_to_call() (in module sgkit)": [[14, "sgkit.convert_probability_to_call"]], "count_call_alleles() (in module sgkit)": [[15, "sgkit.count_call_alleles"]], "count_cohort_alleles() (in module sgkit)": [[16, "sgkit.count_cohort_alleles"]], "count_variant_alleles() (in module sgkit)": [[17, "sgkit.count_variant_alleles"]], "count_variant_genotypes() (in module sgkit)": [[18, "sgkit.count_variant_genotypes"]], "display_genotypes() (in module sgkit)": [[19, "sgkit.display_genotypes"]], "display_pedigree() (in module sgkit)": [[20, "sgkit.display_pedigree"]], "divergence() (in module sgkit)": [[21, "sgkit.divergence"]], "diversity() (in module sgkit)": [[22, "sgkit.diversity"]], "filter_partial_calls() (in module sgkit)": [[23, "sgkit.filter_partial_calls"]], "genee() (in module sgkit)": [[24, "sgkit.genee"]], "genomic_relationship() (in module sgkit)": [[25, "sgkit.genomic_relationship"]], "gwas_linear_regression() (in module sgkit)": [[26, "sgkit.gwas_linear_regression"]], "hardy_weinberg_test() (in module sgkit)": [[27, "sgkit.hardy_weinberg_test"]], "hybrid_inverse_relationship() (in module sgkit)": [[28, "sgkit.hybrid_inverse_relationship"]], "hybrid_relationship() (in module sgkit)": [[29, "sgkit.hybrid_relationship"]], "identity_by_state() (in module sgkit)": [[30, "sgkit.identity_by_state"]], "individual_heterozygosity() (in module sgkit)": [[31, "sgkit.individual_heterozygosity"]], "infer_call_ploidy() (in module sgkit)": [[32, "sgkit.infer_call_ploidy"]], "infer_sample_ploidy() (in module sgkit)": [[33, "sgkit.infer_sample_ploidy"]], "infer_variant_ploidy() (in module sgkit)": [[34, "sgkit.infer_variant_ploidy"]], "invert_relationship_matrix() (in module sgkit)": [[35, "sgkit.invert_relationship_matrix"]], "bgen_to_zarr() (in module sgkit.io.bgen)": [[36, "sgkit.io.bgen.bgen_to_zarr"]], "read_bgen() (in module sgkit.io.bgen)": [[37, "sgkit.io.bgen.read_bgen"]], "rechunk_bgen() (in module sgkit.io.bgen)": [[38, "sgkit.io.bgen.rechunk_bgen"]], "plink_to_zarr() (in module sgkit.io.plink)": [[39, "sgkit.io.plink.plink_to_zarr"]], "read_plink() (in module sgkit.io.plink)": [[40, "sgkit.io.plink.read_plink"]], "write_plink() (in module sgkit.io.plink)": [[41, "sgkit.io.plink.write_plink"]], "zarr_to_plink() (in module sgkit.io.plink)": [[42, "sgkit.io.plink.zarr_to_plink"]], "concat_zarrs() (in module sgkit.io.vcf)": [[43, "sgkit.io.vcf.concat_zarrs"]], "partition_into_regions() (in module sgkit.io.vcf)": [[44, "sgkit.io.vcf.partition_into_regions"]], "read_vcf() (in module sgkit.io.vcf)": [[45, "sgkit.io.vcf.read_vcf"]], "vcf_to_zarr() (in module sgkit.io.vcf)": [[46, "sgkit.io.vcf.vcf_to_zarr"]], "vcf_to_zarrs() (in module sgkit.io.vcf)": [[47, "sgkit.io.vcf.vcf_to_zarrs"]], "write_vcf() (in module sgkit.io.vcf)": [[48, "sgkit.io.vcf.write_vcf"]], "zarr_array_sizes() (in module sgkit.io.vcf)": [[49, "sgkit.io.vcf.zarr_array_sizes"]], "zarr_to_vcf() (in module sgkit.io.vcf)": [[50, "sgkit.io.vcf.zarr_to_vcf"]], "ld_matrix() (in module sgkit)": [[51, "sgkit.ld_matrix"]], "ld_prune() (in module sgkit)": [[52, "sgkit.ld_prune"]], "load_dataset() (in module sgkit)": [[53, "sgkit.load_dataset"]], "maximal_independent_set() (in module sgkit)": [[54, "sgkit.maximal_independent_set"]], "observed_heterozygosity() (in module sgkit)": [[55, "sgkit.observed_heterozygosity"]], "pairwise_distance() (in module sgkit)": [[56, "sgkit.pairwise_distance"]], "parent_indices() (in module sgkit)": [[57, "sgkit.parent_indices"]], "pbs() (in module sgkit)": [[58, "sgkit.pbs"]], "pc_relate() (in module sgkit)": [[59, "sgkit.pc_relate"]], "pedigree_contribution() (in module sgkit)": [[60, "sgkit.pedigree_contribution"]], "pedigree_inbreeding() (in module sgkit)": [[61, "sgkit.pedigree_inbreeding"]], "pedigree_inverse_kinship() (in module sgkit)": [[62, "sgkit.pedigree_inverse_kinship"]], "pedigree_kinship() (in module sgkit)": [[63, "sgkit.pedigree_kinship"]], "pedigree_sel() (in module sgkit)": [[64, "sgkit.pedigree_sel"]], "read_scikit_allel_vcfzarr() (in module sgkit)": [[65, "sgkit.read_scikit_allel_vcfzarr"]], "regenie() (in module sgkit)": [[66, "sgkit.regenie"]], "sample_stats() (in module sgkit)": [[67, "sgkit.sample_stats"]], "save_dataset() (in module sgkit)": [[68, "sgkit.save_dataset"]], "simulate_genedrop() (in module sgkit)": [[69, "sgkit.simulate_genedrop"]], "simulate_genotype_call_dataset() (in module sgkit)": [[70, "sgkit.simulate_genotype_call_dataset"]], "call_allele_count_spec (in module sgkit.variables)": [[71, "sgkit.variables.call_allele_count_spec"]], "call_allele_frequency_spec (in module sgkit.variables)": [[72, "sgkit.variables.call_allele_frequency_spec"]], "call_dosage_mask_spec (in module sgkit.variables)": [[73, "sgkit.variables.call_dosage_mask_spec"]], "call_dosage_spec (in module sgkit.variables)": [[74, "sgkit.variables.call_dosage_spec"]], "call_genotype_complete_mask_spec (in module sgkit.variables)": [[75, "sgkit.variables.call_genotype_complete_mask_spec"]], "call_genotype_complete_spec (in module sgkit.variables)": [[76, "sgkit.variables.call_genotype_complete_spec"]], "call_genotype_fill_spec (in module sgkit.variables)": [[77, "sgkit.variables.call_genotype_fill_spec"]], "call_genotype_index_mask_spec (in module sgkit.variables)": [[78, "sgkit.variables.call_genotype_index_mask_spec"]], "call_genotype_index_spec (in module sgkit.variables)": [[79, "sgkit.variables.call_genotype_index_spec"]], "call_genotype_mask_spec (in module sgkit.variables)": [[80, "sgkit.variables.call_genotype_mask_spec"]], "call_genotype_phased_spec (in module sgkit.variables)": [[81, "sgkit.variables.call_genotype_phased_spec"]], "call_genotype_probability_mask_spec (in module sgkit.variables)": [[82, "sgkit.variables.call_genotype_probability_mask_spec"]], "call_genotype_probability_spec (in module sgkit.variables)": [[83, "sgkit.variables.call_genotype_probability_spec"]], "call_genotype_spec (in module sgkit.variables)": [[84, "sgkit.variables.call_genotype_spec"]], "call_heterozygosity_spec (in module sgkit.variables)": [[85, "sgkit.variables.call_heterozygosity_spec"]], "call_ploidy_spec (in module sgkit.variables)": [[86, "sgkit.variables.call_ploidy_spec"]], "cohort_allele_count_spec (in module sgkit.variables)": [[87, "sgkit.variables.cohort_allele_count_spec"]], "cohort_allele_frequency_spec (in module sgkit.variables)": [[88, "sgkit.variables.cohort_allele_frequency_spec"]], "covariates_spec (in module sgkit.variables)": [[89, "sgkit.variables.covariates_spec"]], "interval_contig_name_spec (in module sgkit.variables)": [[90, "sgkit.variables.interval_contig_name_spec"]], "interval_start_spec (in module sgkit.variables)": [[91, "sgkit.variables.interval_start_spec"]], "interval_stop_spec (in module sgkit.variables)": [[92, "sgkit.variables.interval_stop_spec"]], "ld_prune_index_to_drop_spec (in module sgkit.variables)": [[93, "sgkit.variables.ld_prune_index_to_drop_spec"]], "parent_id_spec (in module sgkit.variables)": [[94, "sgkit.variables.parent_id_spec"]], "parent_spec (in module sgkit.variables)": [[95, "sgkit.variables.parent_spec"]], "pc_relate_phi_spec (in module sgkit.variables)": [[96, "sgkit.variables.pc_relate_phi_spec"]], "regenie_base_prediction_spec (in module sgkit.variables)": [[97, "sgkit.variables.regenie_base_prediction_spec"]], "regenie_loco_prediction_spec (in module sgkit.variables)": [[98, "sgkit.variables.regenie_loco_prediction_spec"]], "regenie_meta_prediction_spec (in module sgkit.variables)": [[99, "sgkit.variables.regenie_meta_prediction_spec"]], "sample_call_rate_spec (in module sgkit.variables)": [[100, "sgkit.variables.sample_call_rate_spec"]], "sample_cohort_spec (in module sgkit.variables)": [[101, "sgkit.variables.sample_cohort_spec"]], "sample_id_spec (in module sgkit.variables)": [[102, "sgkit.variables.sample_id_spec"]], "sample_n_called_spec (in module sgkit.variables)": [[103, "sgkit.variables.sample_n_called_spec"]], "sample_n_het_spec (in module sgkit.variables)": [[104, "sgkit.variables.sample_n_het_spec"]], "sample_n_hom_alt_spec (in module sgkit.variables)": [[105, "sgkit.variables.sample_n_hom_alt_spec"]], "sample_n_hom_ref_spec (in module sgkit.variables)": [[106, "sgkit.variables.sample_n_hom_ref_spec"]], "sample_n_non_ref_spec (in module sgkit.variables)": [[107, "sgkit.variables.sample_n_non_ref_spec"]], "sample_pca_component_spec (in module sgkit.variables)": [[108, "sgkit.variables.sample_pca_component_spec"]], "sample_pca_explained_variance_ratio_spec (in module sgkit.variables)": [[109, "sgkit.variables.sample_pca_explained_variance_ratio_spec"]], "sample_pca_explained_variance_spec (in module sgkit.variables)": [[110, "sgkit.variables.sample_pca_explained_variance_spec"]], "sample_pca_loading_spec (in module sgkit.variables)": [[111, "sgkit.variables.sample_pca_loading_spec"]], "sample_pca_projection_spec (in module sgkit.variables)": [[112, "sgkit.variables.sample_pca_projection_spec"]], "sample_ploidy_spec (in module sgkit.variables)": [[113, "sgkit.variables.sample_ploidy_spec"]], "stat_fst_spec (in module sgkit.variables)": [[114, "sgkit.variables.stat_Fst_spec"]], "stat_garud_h123_spec (in module sgkit.variables)": [[115, "sgkit.variables.stat_Garud_h123_spec"]], "stat_garud_h12_spec (in module sgkit.variables)": [[116, "sgkit.variables.stat_Garud_h12_spec"]], "stat_garud_h1_spec (in module sgkit.variables)": [[117, "sgkit.variables.stat_Garud_h1_spec"]], "stat_garud_h2_h1_spec (in module sgkit.variables)": [[118, "sgkit.variables.stat_Garud_h2_h1_spec"]], "stat_hamilton_kerr_lambda_spec (in module sgkit.variables)": [[119, "sgkit.variables.stat_Hamilton_Kerr_lambda_spec"]], "stat_hamilton_kerr_tau_spec (in module sgkit.variables)": [[120, "sgkit.variables.stat_Hamilton_Kerr_tau_spec"]], "stat_tajimas_d_spec (in module sgkit.variables)": [[121, "sgkit.variables.stat_Tajimas_D_spec"]], "stat_weir_goudet_beta_spec (in module sgkit.variables)": [[122, "sgkit.variables.stat_Weir_Goudet_beta_spec"]], "stat_divergence_spec (in module sgkit.variables)": [[123, "sgkit.variables.stat_divergence_spec"]], "stat_diversity_spec (in module sgkit.variables)": [[124, "sgkit.variables.stat_diversity_spec"]], "stat_genomic_kinship_spec (in module sgkit.variables)": [[125, "sgkit.variables.stat_genomic_kinship_spec"]], "stat_genomic_relationship_spec (in module sgkit.variables)": [[126, "sgkit.variables.stat_genomic_relationship_spec"]], "stat_hybrid_inverse_relationship_spec (in module sgkit.variables)": [[127, "sgkit.variables.stat_hybrid_inverse_relationship_spec"]], "stat_hybrid_relationship_spec (in module sgkit.variables)": [[128, "sgkit.variables.stat_hybrid_relationship_spec"]], "stat_identity_by_state_spec (in module sgkit.variables)": [[129, "sgkit.variables.stat_identity_by_state_spec"]], "stat_inverse_relationship_spec (in module sgkit.variables)": [[130, "sgkit.variables.stat_inverse_relationship_spec"]], "stat_observed_heterozygosity_spec (in module sgkit.variables)": [[131, "sgkit.variables.stat_observed_heterozygosity_spec"]], "stat_pbs_spec (in module sgkit.variables)": [[132, "sgkit.variables.stat_pbs_spec"]], "stat_pedigree_contribution_spec (in module sgkit.variables)": [[133, "sgkit.variables.stat_pedigree_contribution_spec"]], "stat_pedigree_inbreeding_spec (in module sgkit.variables)": [[134, "sgkit.variables.stat_pedigree_inbreeding_spec"]], "stat_pedigree_inverse_kinship_spec (in module sgkit.variables)": [[135, "sgkit.variables.stat_pedigree_inverse_kinship_spec"]], "stat_pedigree_inverse_relationship_spec (in module sgkit.variables)": [[136, "sgkit.variables.stat_pedigree_inverse_relationship_spec"]], "stat_pedigree_kinship_spec (in module sgkit.variables)": [[137, "sgkit.variables.stat_pedigree_kinship_spec"]], "stat_pedigree_relationship_spec (in module sgkit.variables)": [[138, "sgkit.variables.stat_pedigree_relationship_spec"]], "traits_spec (in module sgkit.variables)": [[139, "sgkit.variables.traits_spec"]], "variant_allele_count_spec (in module sgkit.variables)": [[140, 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