Index

_

__add__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.StringExpression method) (hail.vds.combiner.VDSMetadata method) __and__() (hail.expr.BooleanExpression method) (hail.expr.SetExpression method) __class_getitem__ (hail.expr.StructExpression attribute) (hail.expr.TupleExpression attribute) __class_getitem__() (hail.vds.combiner.VDSMetadata method) __contains__() (hail.vds.combiner.VDSMetadata method) __eq__() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.vds.combiner.VariantDatasetCombiner method) (hail.vds.combiner.VDSMetadata method) __floordiv__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) __ge__() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.vds.combiner.VDSMetadata method) __getitem__() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CallExpression method) (hail.expr.DictExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.vds.combiner.VDSMetadata method) __getnewargs__() (hail.vds.combiner.VDSMetadata method) __gt__() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.vds.combiner.VDSMetadata method) __invert__() (hail.expr.BooleanExpression method) __iter__() (hail.vds.combiner.VDSMetadata method) __le__() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.vds.combiner.VDSMetadata method)

__len__() (hail.expr.TupleExpression method) (hail.vds.combiner.VDSMetadata method) __lt__() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.vds.combiner.VDSMetadata method) __matmul__() (hail.expr.NDArrayNumericExpression method) __mod__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NumericExpression method) __mul__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.vds.combiner.VDSMetadata method) __ne__() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.vds.combiner.VDSMetadata method) __neg__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) __or__() (hail.expr.BooleanExpression method) (hail.expr.SetExpression method) __pow__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NumericExpression method) __rmul__() (hail.vds.combiner.VDSMetadata method) __sub__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) __truediv__() (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) __xor__() (hail.expr.SetExpression method) _logistic_skat() (in module hail.methods)

A

abs() (hail.linalg.BlockMatrix method) (in module hail.expr.functions) add() (hail.expr.SetExpression method) add_col_index() (hail.MatrixTable method) add_index() (hail.Table method) add_liftover() (hail.genetics.ReferenceGenome method) add_row_index() (hail.MatrixTable method) add_sequence() (hail.genetics.ReferenceGenome method) aes() (in module hail.ggplot) Aesthetic (class in hail.ggplot) agg_fields() (in module hail.experimental.ldscsim) aggregate() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.GroupedMatrixTable method) (hail.GroupedTable method) (hail.Table method) aggregate_cols() (hail.GroupedMatrixTable method) (hail.MatrixTable method) aggregate_entries() (hail.GroupedMatrixTable method) (hail.MatrixTable method) aggregate_rows() (hail.GroupedMatrixTable method) (hail.MatrixTable method) all() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (hail.Table method) (in module hail.expr.aggregators) (in module hail.expr.functions) allele_type() (in module hail.expr.functions) alleles (hail.genetics.Call property) AlleleType (class in hail.genetics) annotate() (hail.expr.StructExpression method) (hail.Table method) annotate_all() (in module hail.experimental.ldscsim) annotate_cols() (hail.MatrixTable method)

annotate_entries() (hail.MatrixTable method) annotate_globals() (hail.MatrixTable method) (hail.Table method) annotate_rows() (hail.MatrixTable method) annotate_rows_db() (hail.experimental.DB method) anti_join() (hail.Table method) anti_join_cols() (hail.MatrixTable method) anti_join_rows() (hail.MatrixTable method) any() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (hail.Table method) (in module hail.expr.aggregators) (in module hail.expr.functions) ANY_REGION (in module hail.utils) append() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) approx_cdf() (in module hail.expr.aggregators) approx_equal() (in module hail.expr.functions) approx_median() (in module hail.expr.aggregators) approx_quantiles() (in module hail.expr.aggregators) arange() (in module hail.nd) argmax() (in module hail.expr.functions) argmin() (in module hail.expr.functions) array() (in module hail.expr.functions) (in module hail.nd) array_agg() (in module hail.expr.aggregators) array_scan() (in module hail.expr.functions) array_sum() (in module hail.expr.aggregators) array_windows() (in module hail.linalg.utils) ArrayExpression (class in hail.expr) ArrayNumericExpression (class in hail.expr) asc() (in module hail) ascertainment_bias() (in module hail.experimental.ldscsim) available_datasets (hail.experimental.DB property)

B

balding_nichols_model() (in module hail.methods) binarize() (in module hail.experimental.ldscsim) binary_search() (in module hail.expr.functions) bind() (in module hail.expr.functions) binom_test() (in module hail.expr.functions) bit_and() (in module hail.expr.functions) bit_count() (in module hail.expr.functions) bit_lshift() (in module hail.expr.functions)

bit_not() (in module hail.expr.functions) bit_or() (in module hail.expr.functions) bit_rshift() (in module hail.expr.functions) bit_xor() (in module hail.expr.functions) block_size (hail.linalg.BlockMatrix property) BlockMatrix (class in hail.linalg) bool() (in module hail.expr.functions) BooleanExpression (class in hail.expr)

C

cache() (hail.linalg.BlockMatrix method) (hail.MatrixTable method) (hail.Table method) calculate_phenotypes() (in module hail.experimental.ldscsim) Call (class in hail.genetics) call() (in module hail.expr.functions) call_stats() (in module hail.expr.aggregators) CallExpression (class in hail.expr) case() (in module hail.expr.functions) CaseBuilder (class in hail.expr.builders) cdf() (in module hail.plot) ceil() (hail.linalg.BlockMatrix method) (in module hail.expr.functions) checkpoint() (hail.linalg.BlockMatrix method) (hail.MatrixTable method) (hail.Table method) (hail.vds.VariantDataset method) chi_squared_test() (in module hail.expr.functions) choose_cols() (hail.MatrixTable method) citation() (in module hail) coalesce() (in module hail.expr.functions) cochran_mantel_haenszel_test() (in module hail.expr.functions) col (hail.MatrixTable property) col_key (hail.MatrixTable property) col_value (hail.MatrixTable property) collect() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.Table method) (in module hail.expr.aggregators)

collect_as_set() (in module hail.expr.aggregators) collect_by_key() (hail.Table method) collect_cols_by_key() (hail.MatrixTable method) CollectionExpression (class in hail.expr) cols() (hail.MatrixTable method) complete_trios() (hail.genetics.Pedigree method) COMPLEX (hail.genetics.AlleleType attribute) compute_charr() (in module hail.methods) compute_entry_filter_stats() (hail.MatrixTable method) concatenate() (in module hail.nd) concordance() (in module hail.methods) cond() (in module hail.expr.functions) contains() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.DictExpression method) (hail.expr.IntervalExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) contains_allele() (hail.expr.CallExpression method) contig (hail.expr.LocusExpression property) (hail.genetics.Locus property) contig_idx (hail.expr.LocusExpression property) contig_length() (hail.genetics.ReferenceGenome method) (in module hail.expr.functions) contigs (hail.genetics.ReferenceGenome property) contingency_table_test() (in module hail.expr.functions) coord_cartesian() (in module hail.ggplot) copy() (in module hailtop.fs) copy_log() (in module hail.utils) corr() (in module hail.expr.aggregators) (in module hail.expr.functions) count() (hail.expr.TupleExpression method) (hail.MatrixTable method) (hail.Table method) (hail.vds.combiner.VDSMetadata method) (in module hail.expr.aggregators) count_cols() (hail.MatrixTable method) count_rows() (hail.MatrixTable method) count_where() (in module hail.expr.aggregators) counter() (in module hail.expr.aggregators) cumulative_histogram() (in module hail.plot) cumulative_sum() (in module hail.expr.functions)

D

DB (class in hail.experimental) dbeta() (in module hail.expr.functions) dchisq() (in module hail.expr.functions) de_novo() (in module hail.methods) default() (hail.expr.builders.CaseBuilder method) (hail.expr.builders.SwitchBuilder method) default_block_size() (hail.linalg.BlockMatrix static method) default_exome_interval_size (hail.vds.combiner.VariantDatasetCombiner attribute) default_genome_interval_size (hail.vds.combiner.VariantDatasetCombiner attribute) default_reference() (in module hail) DELETION (hail.genetics.AlleleType attribute) delimit() (in module hail.expr.functions) densify() (hail.linalg.BlockMatrix method) desc() (in module hail) describe() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.GroupedMatrixTable method) (hail.MatrixTable method) (hail.Table method)

diagonal() (hail.linalg.BlockMatrix method) (in module hail.nd) dict() (in module hail.expr.functions) DictExpression (class in hail.expr) difference() (hail.expr.SetExpression method) distinct() (hail.Table method) distinct_by_col() (hail.MatrixTable method) distinct_by_row() (hail.MatrixTable method) dnorm() (in module hail.expr.functions) downcode() (in module hail.expr.functions) downsample() (in module hail.expr.aggregators) dpois() (in module hail.expr.functions) drop() (hail.expr.StructExpression method) (hail.MatrixTable method) (hail.Table method) dtype (hail.expr.ArrayExpression property) (hail.expr.ArrayNumericExpression property) (hail.expr.BooleanExpression property) (hail.expr.CallExpression property) (hail.expr.CollectionExpression property) (hail.expr.DictExpression property) (hail.expr.Expression property) (hail.expr.Float32Expression property) (hail.expr.Float64Expression property) (hail.expr.Int32Expression property) (hail.expr.Int64Expression property) (hail.expr.IntervalExpression property) (hail.expr.LocusExpression property) (hail.expr.NDArrayExpression property) (hail.expr.NDArrayNumericExpression property) (hail.expr.NumericExpression property) (hail.expr.SetExpression property) (hail.expr.StringExpression property) (hail.expr.StructExpression property) (hail.expr.TupleExpression property) dtype() (in module hail.expr.types)

E

element_type (hail.linalg.BlockMatrix property) empty_array() (in module hail.expr.functions) empty_dict() (in module hail.expr.functions) empty_set() (in module hail.expr.functions) end (hail.expr.IntervalExpression property) endswith() (hail.expr.StringExpression method) entries() (hail.linalg.BlockMatrix method) (hail.MatrixTable method) entropy() (in module hail.expr.functions) entry (hail.MatrixTable property) enumerate() (in module hail.expr.functions) eval() (in module hail.expr) exists() (in module hailtop.fs) exp() (in module hail.expr.functions) expand_types() (hail.Table method) expit() (in module hail.expr.functions) explode() (hail.Table method) (in module hail.expr.aggregators) explode_cols() (hail.MatrixTable method) explode_rows() (hail.MatrixTable method) explode_trio_matrix() (in module hail.experimental) export() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.linalg.BlockMatrix static method) (hail.Table method)

export_bgen() (in module hail.methods) export_blocks() (hail.linalg.BlockMatrix method) export_elasticsearch() (in module hail.methods) export_entries_by_col() (in module hail.experimental) export_gen() (in module hail.methods) export_plink() (in module hail.methods) export_rectangles() (hail.linalg.BlockMatrix method) export_vcf() (in module hail.methods) Expression (class in hail.expr) extend() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) eye() (in module hail.nd)

F

facet_wrap() (in module hail.ggplot) fam_id (hail.genetics.Trio property) FigureAttribute (class in hail.ggplot) fill() (hail.linalg.BlockMatrix class method) filter() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (hail.linalg.BlockMatrix method) (hail.Table method) (in module hail.expr.aggregators) (in module hail.expr.functions) filter_alleles() (in module hail.methods) filter_alleles_hts() (in module hail.methods) filter_chromosomes() (in module hail.vds) filter_cols() (hail.linalg.BlockMatrix method) (hail.MatrixTable method) filter_entries() (hail.MatrixTable method) filter_intervals() (in module hail.methods) (in module hail.vds) filter_rows() (hail.linalg.BlockMatrix method) (hail.MatrixTable method) filter_samples() (in module hail.vds) filter_to() (hail.genetics.Pedigree method) filter_variants() (in module hail.vds) filtering_allele_frequency() (in module hail.experimental) find() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (in module hail.expr.functions) finished (hail.vds.combiner.VariantDatasetCombiner property) first() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) first_match_in() (hail.expr.StringExpression method)

fisher_exact_test() (in module hail.expr.functions) flatmap() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (in module hail.expr.functions) flatten() (hail.expr.StructExpression method) (hail.Table method) (in module hail.expr.functions) float() (in module hail.expr.functions) float32() (in module hail.expr.functions) Float32Expression (class in hail.expr) float64() (in module hail.expr.functions) Float64Expression (class in hail.expr) floor() (hail.linalg.BlockMatrix method) (in module hail.expr.functions) fold() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (in module hail.expr.functions) format() (in module hail.expr.functions) fraction() (in module hail.expr.aggregators) from_entry_expr() (hail.linalg.BlockMatrix class method) from_fasta_file() (hail.genetics.ReferenceGenome class method) from_merged_representation() (hail.vds.VariantDataset static method) from_ndarray() (hail.linalg.BlockMatrix class method) from_numpy() (hail.linalg.BlockMatrix class method) from_pandas() (hail.Table static method) from_parts() (hail.MatrixTable static method) from_rows_table() (hail.MatrixTable class method) from_spark() (hail.Table static method) fromfile() (hail.linalg.BlockMatrix class method) frozendict (class in hail.utils) full() (in module hail.nd) full_outer_join_mt() (in module hail.experimental)

G

gather() (in module hail.experimental) genetic_relatedness_matrix() (in module hail.methods) geom_area() (in module hail.ggplot) geom_bar() (in module hail.ggplot) geom_col() (in module hail.ggplot) geom_density() (in module hail.ggplot) geom_histogram() (in module hail.ggplot) geom_hline() (in module hail.ggplot) geom_line() (in module hail.ggplot) geom_point() (in module hail.ggplot) geom_ribbon() (in module hail.ggplot) geom_text() (in module hail.ggplot) geom_vline() (in module hail.ggplot) get() (hail.expr.DictExpression method) (hail.expr.StructExpression method) get_1kg() (in module hail.utils) get_coef_dict() (in module hail.experimental.ldscsim) get_cov_matrix() (in module hail.experimental.ldscsim) get_gene_intervals() (in module hail.experimental) get_hgdp() (in module hail.utils) get_movie_lens() (in module hail.utils) get_reference() (in module hail) get_sequence() (in module hail.expr.functions) get_vcf_metadata() (in module hail.methods) GGPlot (class in hail.ggplot)

ggplot() (in module hail.ggplot) ggtitle() (in module hail.ggplot) global_position() (hail.expr.LocusExpression method) global_positions_dict (hail.genetics.ReferenceGenome property) globals (hail.MatrixTable property) (hail.Table property) globals_table() (hail.MatrixTable method) gp_dosage() (in module hail.expr.functions) grep() (in module hail.methods) group_by() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (hail.Table method) (in module hail.expr.aggregators) (in module hail.expr.functions) group_cols_by() (hail.GroupedMatrixTable method) (hail.MatrixTable method) group_rows_by() (hail.GroupedMatrixTable method) (hail.MatrixTable method) grouped() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) GroupedMatrixTable (class in hail) GroupedTable (class in hail) gvcf_batch_size (hail.vds.combiner.VariantDatasetCombiner property)

H

hadoop_copy() (in module hail.utils) hadoop_exists() (in module hail.utils) hadoop_is_dir() (in module hail.utils) hadoop_is_file() (in module hail.utils) hadoop_ls() (in module hail.utils) hadoop_open() (in module hail.utils) hadoop_scheme_supported() (in module hail.utils) hadoop_stat() (in module hail.utils) hail_metadata() (in module hail.experimental) HailType (class in hail.expr.types) hamming() (in module hail.expr.functions) hardy_weinberg_test() (in module hail.expr.aggregators) (in module hail.expr.functions)

has_liftover() (hail.genetics.ReferenceGenome method) has_sequence() (hail.genetics.ReferenceGenome method) head() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.MatrixTable method) (hail.Table method) hist() (in module hail.expr.aggregators) histogram() (in module hail.plot) histogram2d() (in module hail.plot) hstack() (in module hail.nd) hwe_normalized_pca() (in module hail.methods)

I

identity() (in module hail.nd) identity_by_descent() (in module hail.methods) if_else() (in module hail.expr.functions) import_bed() (in module hail.methods) import_bgen() (in module hail.methods) import_fam() (in module hail.methods) import_gen() (in module hail.methods) import_gtf() (in module hail.experimental) import_lines() (in module hail.methods) import_locus_intervals() (in module hail.methods) import_matrix_table() (in module hail.methods) import_plink() (in module hail.methods) import_table() (in module hail.methods) import_vcf() (in module hail.methods) impute_sex() (in module hail.methods) impute_sex_chr_ploidy_from_interval_coverage() (in module hail.vds) impute_sex_chromosome_ploidy() (in module hail.vds) in_autosome() (hail.expr.LocusExpression method) in_autosome_or_par() (hail.expr.LocusExpression method) in_mito() (hail.expr.LocusExpression method) in_x_nonpar() (hail.expr.LocusExpression method) in_x_par() (hail.expr.LocusExpression method) in_y_nonpar() (hail.expr.LocusExpression method) in_y_par() (hail.expr.LocusExpression method) inbreeding() (in module hail.expr.aggregators) includes_end (hail.expr.IntervalExpression property) includes_start (hail.expr.IntervalExpression property) index() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.TupleExpression method) (hail.Table method) (hail.vds.combiner.VDSMetadata method) index_bgen() (in module hail.methods) index_cols() (hail.MatrixTable method) index_entries() (hail.MatrixTable method) index_globals() (hail.MatrixTable method) (hail.Table method) index_rows() (hail.MatrixTable method) info_score() (in module hail.expr.aggregators) init() (in module hail) INSERTION (hail.genetics.AlleleType attribute) int() (in module hail.expr.functions) int32() (in module hail.expr.functions) Int32Expression (class in hail.expr) int64() (in module hail.expr.functions) Int64Expression (class in hail.expr) intersection() (hail.expr.SetExpression method)

Interval (class in hail.utils) interval() (in module hail.expr.functions) interval_coverage() (in module hail.vds) IntervalExpression (class in hail.expr) inv() (in module hail.nd) is_complete() (hail.genetics.Trio method) is_complex() (in module hail.expr.functions) is_defined() (in module hail.expr.functions) is_deletion() (in module hail.expr.functions) is_diploid() (hail.expr.CallExpression method) (hail.genetics.Call method) is_dir() (in module hailtop.fs) is_female (hail.genetics.Trio property) is_file() (in module hailtop.fs) is_finite() (in module hail.expr.functions) is_haploid() (hail.expr.CallExpression method) (hail.genetics.Call method) is_het() (hail.expr.CallExpression method) (hail.genetics.Call method) is_het_non_ref() (hail.expr.CallExpression method) (hail.genetics.Call method) is_het_ref() (hail.expr.CallExpression method) (hail.genetics.Call method) is_hom_ref() (hail.expr.CallExpression method) (hail.genetics.Call method) is_hom_var() (hail.expr.CallExpression method) (hail.genetics.Call method) is_indel() (in module hail.expr.functions) is_infinite() (in module hail.expr.functions) is_insertion() (in module hail.expr.functions) is_male (hail.genetics.Trio property) is_missing() (in module hail.expr.functions) is_mnp() (in module hail.expr.functions) is_nan() (in module hail.expr.functions) is_non_ref() (hail.expr.CallExpression method) (hail.genetics.Call method) is_snp() (in module hail.expr.functions) is_sparse (hail.linalg.BlockMatrix property) is_star() (in module hail.expr.functions) is_strand_ambiguous() (in module hail.expr.functions) is_subset() (hail.expr.SetExpression method) is_transition() (in module hail.expr.functions) is_transversion() (in module hail.expr.functions) is_valid_contig() (in module hail.expr.functions) is_valid_locus() (in module hail.expr.functions) items() (hail.expr.DictExpression method) (hail.expr.StructExpression method)

J

join() (hail.expr.StringExpression method) (hail.Table method)

json() (in module hail.expr.functions)

K

key (hail.Table property) key_by() (hail.Table method) key_cols_by() (hail.MatrixTable method) key_rows_by() (hail.MatrixTable method) key_set() (hail.expr.DictExpression method)

keyed_intersection() (in module hail.expr.functions) keyed_union() (in module hail.expr.functions) keys() (hail.expr.DictExpression method) (hail.expr.StructExpression method) king() (in module hail.methods)

L

lambda_gc() (in module hail.methods) last() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) ld_matrix() (in module hail.methods) ld_prune() (in module hail.methods) ld_score() (in module hail.experimental) ld_score_regression() (in module hail.experimental) len() (in module hail.expr.functions) length() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) lengths (hail.genetics.ReferenceGenome property) lgt_to_gt() (in module hail.vds) liftover() (in module hail.expr.functions) linear_mixed_model() (in module hail.methods) linear_mixed_regression_rows() (in module hail.methods) linear_regression_rows() (in module hail.methods) LinearMixedModel (class in hail.stats) linreg() (in module hail.expr.aggregators)

literal() (in module hail.expr.functions) load() (hail.vds.combiner.VariantDatasetCombiner static method) load_combiner() (in module hail.vds.combiner) load_dataset() (in module hail.experimental) local_to_global() (in module hail.vds) localize_entries() (hail.MatrixTable method) Locus (class in hail.genetics) locus() (in module hail.expr.functions) locus_from_global_position() (hail.genetics.ReferenceGenome method) (in module hail.expr.functions) locus_interval() (in module hail.expr.functions) locus_windows() (in module hail.linalg.utils) LocusExpression (class in hail.expr) log() (hail.linalg.BlockMatrix method) (in module hail.expr.functions) log10() (in module hail.expr.functions) logistic_regression_rows() (in module hail.methods) logit() (in module hail.expr.functions) loop() (in module hail.experimental) lower() (hail.expr.StringExpression method) ls() (in module hailtop.fs)

M

make_betas() (in module hail.experimental.ldscsim) make_table() (hail.MatrixTable method) manhattan() (in module hail.plot) map() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.SetExpression method) (in module hail.expr.functions) map2() (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) map_values() (hail.expr.DictExpression method) mat_id (hail.genetics.Trio property) matches() (hail.expr.StringExpression method) MatrixTable (class in hail) max() (in module hail.expr.aggregators) (in module hail.expr.functions)

maximal_independent_set() (in module hail.methods) maximum() (in module hail.nd) mean() (in module hail.expr.aggregators) (in module hail.expr.functions) median() (in module hail.expr.functions) mendel_error_code() (in module hail.expr.functions) mendel_errors() (in module hail.methods) merge_reference_blocks() (in module hail.vds) min() (in module hail.expr.aggregators) (in module hail.expr.functions) min_rep() (in module hail.expr.functions) minimum() (in module hail.nd) missing() (in module hail.expr.functions) mkdir() (in module hailtop.fs) MNP (hail.genetics.AlleleType attribute) mt_contigs (hail.genetics.ReferenceGenome property) multi_way_zip_join() (hail.Table static method) multitrait_inf() (in module hail.experimental.ldscsim) multitrait_ss() (in module hail.experimental.ldscsim)

N

n_alt_alleles() (hail.expr.CallExpression method) (hail.genetics.Call method) n_cols (hail.linalg.BlockMatrix property) n_partitions() (hail.MatrixTable method) (hail.Table method) n_rows (hail.linalg.BlockMatrix property) n_samples (hail.vds.combiner.VDSMetadata attribute) n_samples() (hail.vds.VariantDataset method) naive_coalesce() (hail.MatrixTable method) (hail.Table method) name (hail.genetics.ReferenceGenome property)

nanmax() (in module hail.expr.functions) nanmin() (in module hail.expr.functions) NDArrayExpression (class in hail.expr) NDArrayNumericExpression (class in hail.expr) ndim (hail.expr.NDArrayExpression property) (hail.expr.NDArrayNumericExpression property) new_combiner() (in module hail.vds.combiner) nirvana() (in module hail.methods) normalize_genotypes() (in module hail.experimental.ldscsim) null() (in module hail.expr.functions) numeric_allele_type() (in module hail.expr.functions) NumericExpression (class in hail.expr)

O

one_hot_alleles() (hail.expr.CallExpression method) (hail.genetics.Call method) ones() (in module hail.nd) open() (in module hailtop.fs) or_else() (in module hail.expr.functions) or_error() (hail.expr.builders.CaseBuilder method) (hail.expr.builders.SwitchBuilder method)

or_missing() (hail.expr.builders.CaseBuilder method) (hail.expr.builders.SwitchBuilder method) (in module hail.expr.functions) order_by() (hail.Table method) output_notebook() (in module hail.plot) overlaps() (hail.expr.IntervalExpression method)

P

par (hail.genetics.ReferenceGenome property) parallelize() (hail.Table class method) parse() (hail.genetics.Locus class method) parse_call() (in module hail.expr.functions) parse_float() (in module hail.expr.functions) parse_float32() (in module hail.expr.functions) parse_float64() (in module hail.expr.functions) parse_int() (in module hail.expr.functions) parse_int32() (in module hail.expr.functions) parse_int64() (in module hail.expr.functions) parse_json() (in module hail.expr.functions) parse_locus() (in module hail.expr.functions) parse_locus_interval() (in module hail.expr.functions) parse_variant() (in module hail.expr.functions) partition_hint() (hail.GroupedMatrixTable method) (hail.GroupedTable method) pat_id (hail.genetics.Trio property) path (hail.vds.combiner.VDSMetadata attribute) pc_project() (in module hail.experimental) pc_relate() (in module hail.methods) pca() (in module hail.methods) pchisqtail() (in module hail.expr.functions) pdf() (in module hail.plot)

Pedigree (class in hail.genetics) persist() (hail.linalg.BlockMatrix method) (hail.MatrixTable method) (hail.Table method) pF() (in module hail.expr.functions) pgenchisq() (in module hail.expr.functions) phase_by_transmission() (in module hail.experimental) phase_trio_matrix_by_transmission() (in module hail.experimental) phased (hail.expr.CallExpression property) (hail.genetics.Call property) pl_dosage() (in module hail.expr.functions) ploidy (hail.expr.CallExpression property) (hail.genetics.Call property) plot_roc_curve() (in module hail.experimental) pnorm() (in module hail.expr.functions) poisson_regression_rows() (in module hail.methods) position (hail.expr.LocusExpression property) (hail.genetics.Locus property) ppois() (in module hail.expr.functions) pretty_name (hail.genetics.AlleleType property) product() (in module hail.expr.aggregators) (in module hail.expr.functions) pT() (in module hail.expr.functions)

Q

qchisqtail() (in module hail.expr.functions) qnorm() (in module hail.expr.functions) qpois() (in module hail.expr.functions)

qq() (in module hail.plot) qr() (in module hail.nd) query_table() (in module hail.expr.functions)

R

rand_beta() (in module hail.expr.functions) rand_bool() (in module hail.expr.functions) rand_cat() (in module hail.expr.functions) rand_dirichlet() (in module hail.expr.functions) rand_gamma() (in module hail.expr.functions) rand_int32() (in module hail.expr.functions) rand_int64() (in module hail.expr.functions) rand_norm() (in module hail.expr.functions) rand_pois() (in module hail.expr.functions) rand_unif() (in module hail.expr.functions) random() (hail.linalg.BlockMatrix class method) range() (in module hail.expr.functions) range_matrix_table() (in module hail.utils) range_table() (in module hail.utils) rbind() (in module hail.expr.functions) read() (hail.genetics.Pedigree class method) (hail.genetics.ReferenceGenome class method) (hail.linalg.BlockMatrix class method) read_expression() (in module hail.experimental) read_matrix_table() (in module hail.methods) read_table() (in module hail.methods) read_vds() (in module hail.vds) realized_relationship_matrix() (in module hail.methods) rectangles_to_numpy() (hail.linalg.BlockMatrix static method) ref_block_max_length_field (hail.vds.VariantDataset attribute) reference_genome (hail.expr.types.tlocus attribute) (hail.genetics.Locus property) (hail.vds.VariantDataset property)

ReferenceGenome (class in hail.genetics) remove() (hail.expr.SetExpression method) (in module hailtop.fs) remove_liftover() (hail.genetics.ReferenceGenome method) remove_sequence() (hail.genetics.ReferenceGenome method) rename() (hail.expr.StructExpression method) (hail.MatrixTable method) (hail.Table method) rename_duplicates() (in module hail.methods) repartition() (hail.MatrixTable method) (hail.Table method) replace() (hail.expr.StringExpression method) reset_global_randomness() (in module hail) reshape() (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) result() (hail.GroupedMatrixTable method) reverse() (hail.expr.StringExpression method) reverse_complement() (in module hail.expr.functions) reversed() (in module hail.expr.functions) rmtree() (in module hailtop.fs) row (hail.MatrixTable property) (hail.Table property) row_correlation() (in module hail.methods) row_key (hail.MatrixTable property) row_value (hail.MatrixTable property) (hail.Table property) rows() (hail.MatrixTable method) run() (hail.vds.combiner.VariantDatasetCombiner method)

S

s (hail.genetics.Trio property) sample() (hail.Table method) sample_cols() (hail.MatrixTable method) sample_qc() (in module hail.methods) (in module hail.vds) sample_rows() (hail.MatrixTable method) save() (hail.vds.combiner.VariantDatasetCombiner method) scale_color_continuous() (in module hail.ggplot) scale_color_discrete() (in module hail.ggplot) scale_color_hue() (in module hail.ggplot) scale_color_identity() (in module hail.ggplot) scale_color_manual() (in module hail.ggplot) scale_fill_continuous() (in module hail.ggplot) scale_fill_discrete() (in module hail.ggplot) scale_fill_hue() (in module hail.ggplot) scale_fill_identity() (in module hail.ggplot) scale_fill_manual() (in module hail.ggplot) scale_x_continuous() (in module hail.ggplot) scale_x_discrete() (in module hail.ggplot) scale_x_genomic() (in module hail.ggplot) scale_x_log10() (in module hail.ggplot) scale_x_reverse() (in module hail.ggplot) scale_y_continuous() (in module hail.ggplot) scale_y_discrete() (in module hail.ggplot) scale_y_log10() (in module hail.ggplot) scale_y_reverse() (in module hail.ggplot) scan() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) scatter() (in module hail.plot) segment_intervals() (in module hail.methods) select() (hail.expr.StructExpression method) (hail.Table method) select_cols() (hail.MatrixTable method) select_entries() (hail.MatrixTable method) select_globals() (hail.MatrixTable method) (hail.Table method) select_rows() (hail.MatrixTable method) semi_join() (hail.Table method) semi_join_cols() (hail.MatrixTable method) semi_join_rows() (hail.MatrixTable method) separate() (in module hail.experimental) sequence_context() (hail.expr.LocusExpression method) set() (in module hail.expr.functions) set_global_seed() (in module hail) SetExpression (class in hail.expr) shape (hail.expr.NDArrayExpression property) (hail.expr.NDArrayNumericExpression property) (hail.linalg.BlockMatrix property) show() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.ggplot.GGPlot method) (hail.MatrixTable method) (hail.Table method) shuffle() (in module hail.expr.functions) sign() (in module hail.expr.functions) simulate_phenotypes() (in module hail.experimental.ldscsim) simulate_random_mating() (in module hail.methods) size() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.SetExpression method)

skat() (in module hail.methods) smoothed_pdf() (in module hail.plot) SNP (hail.genetics.AlleleType attribute) solve() (in module hail.nd) solve_triangular() (in module hail.nd) sorted() (in module hail.expr.functions) spark_context() (in module hail) sparsify_band() (hail.linalg.BlockMatrix method) sparsify_rectangles() (hail.linalg.BlockMatrix method) sparsify_row_intervals() (hail.linalg.BlockMatrix method) sparsify_triangle() (hail.linalg.BlockMatrix method) split() (hail.expr.StringExpression method) split_multi() (in module hail.methods) (in module hail.vds) split_multi_hts() (in module hail.methods) spread() (in module hail.experimental) sqrt() (hail.linalg.BlockMatrix method) (in module hail.expr.functions) STAR (hail.genetics.AlleleType attribute) starmap() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.CollectionExpression method) (hail.expr.SetExpression method) (in module hail.expr.functions) start (hail.expr.IntervalExpression property) startswith() (hail.expr.StringExpression method) stat() (in module hailtop.fs) stats() (in module hail.expr.aggregators) step() (hail.vds.combiner.VariantDatasetCombiner method) stop() (in module hail) store_ref_block_max_length() (in module hail.vds) str() (in module hail.expr.functions) strftime() (in module hail.experimental) StringExpression (class in hail.expr) strings() (hail.genetics.AlleleType static method) strip() (hail.expr.StringExpression method) strptime() (in module hail.experimental) Struct (class in hail.utils) struct() (in module hail.expr.functions) StructExpression (class in hail.expr) sum() (hail.expr.NDArrayNumericExpression method) (hail.linalg.BlockMatrix method) (in module hail.expr.aggregators) (in module hail.expr.functions) summarize() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.MatrixTable method) (hail.Table method) summarize_variants() (in module hail.methods) svd() (hail.linalg.BlockMatrix method) (in module hail.nd) switch() (in module hail.expr.functions) SwitchBuilder (class in hail.expr.builders) SYMBOLIC (hail.genetics.AlleleType attribute)

T

T (hail.expr.NDArrayExpression property) (hail.expr.NDArrayNumericExpression property) (hail.linalg.BlockMatrix property) Table (class in hail) tail() (hail.MatrixTable method) (hail.Table method) take() (hail.expr.ArrayExpression method) (hail.expr.ArrayNumericExpression method) (hail.expr.BooleanExpression method) (hail.expr.CallExpression method) (hail.expr.CollectionExpression method) (hail.expr.DictExpression method) (hail.expr.Expression method) (hail.expr.Float32Expression method) (hail.expr.Float64Expression method) (hail.expr.Int32Expression method) (hail.expr.Int64Expression method) (hail.expr.IntervalExpression method) (hail.expr.LocusExpression method) (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) (hail.expr.NumericExpression method) (hail.expr.SetExpression method) (hail.expr.StringExpression method) (hail.expr.StructExpression method) (hail.expr.TupleExpression method) (hail.Table method) (in module hail.expr.aggregators) tarray (class in hail.expr.types) tbool (in module hail.expr.types) tcall (in module hail.expr.types) tdict (class in hail.expr.types) tfloat (in module hail.expr.types) tfloat32 (in module hail.expr.types) tfloat64 (in module hail.expr.types) tint (in module hail.expr.types) tint32 (in module hail.expr.types) tint64 (in module hail.expr.types) tinterval (class in hail.expr.types)

tlocus (class in hail.expr.types) tmp_dir() (in module hail) tndarray (class in hail.expr.types) to_dense_mt() (in module hail.vds) to_dict() (hail.vds.combiner.VariantDatasetCombiner method) to_matrix_table() (hail.Table method) to_matrix_table_row_major() (hail.linalg.BlockMatrix method) (hail.Table method) to_merged_sparse_mt() (in module hail.vds) to_ndarray() (hail.linalg.BlockMatrix method) to_numpy() (hail.linalg.BlockMatrix method) to_pandas() (hail.Table method) to_plotly() (hail.ggplot.GGPlot method) to_spark() (hail.Table method) to_table_row_major() (hail.linalg.BlockMatrix method) tofile() (hail.linalg.BlockMatrix method) TRANSITION (hail.genetics.AlleleType attribute) translate() (hail.expr.StringExpression method) transmission_disequilibrium_test() (in module hail.methods) transmute() (hail.Table method) transmute_cols() (hail.MatrixTable method) transmute_entries() (hail.MatrixTable method) transmute_globals() (hail.MatrixTable method) (hail.Table method) transmute_rows() (hail.MatrixTable method) transpose() (hail.expr.NDArrayExpression method) (hail.expr.NDArrayNumericExpression method) TRANSVERSION (hail.genetics.AlleleType attribute) tree_matmul() (hail.linalg.BlockMatrix method) triangle() (in module hail.expr.functions) Trio (class in hail.genetics) trio_matrix() (in module hail.methods) trios (hail.genetics.Pedigree property) truncate_reference_blocks() (in module hail.vds) tset (class in hail.expr.types) tstr (in module hail.expr.types) tstruct (class in hail.expr.types) ttuple (class in hail.expr.types) tuple() (in module hail.expr.functions) TupleExpression (class in hail.expr)

U

unfilter_entries() (hail.MatrixTable method) union() (hail.expr.SetExpression method) (hail.Table method) union_cols() (hail.MatrixTable method) union_rows() (hail.MatrixTable method) (hail.vds.VariantDataset method) uniroot() (in module hail.expr.functions) UNKNOWN (hail.genetics.AlleleType attribute)

unpersist() (hail.linalg.BlockMatrix method) (hail.MatrixTable method) (hail.Table method) unphase() (hail.expr.CallExpression method) unphased_diploid_gt_index() (hail.expr.CallExpression method) (hail.genetics.Call method) unphased_diploid_gt_index_call() (in module hail.expr.functions) upper() (hail.expr.StringExpression method)

V

validate() (hail.vds.VariantDataset method) values() (hail.expr.DictExpression method) (hail.expr.StructExpression method) variant_qc() (in module hail.methods) variant_str() (in module hail.expr.functions) VariantDataset (class in hail.vds) VariantDatasetCombiner (class in hail.vds.combiner) vars() (in module hail.ggplot)

VDSMetadata (class in hail.vds.combiner) vep() (in module hail.methods) VEPConfig (class in hail.methods) VEPConfigGRCh37Version85 (class in hail.methods) VEPConfigGRCh38Version95 (class in hail.methods) version() (in module hail) visualize_missingness() (in module hail.plot) vstack() (in module hail.nd)

W

when() (hail.expr.builders.CaseBuilder method) (hail.expr.builders.SwitchBuilder method) when_missing() (hail.expr.builders.SwitchBuilder method) window() (hail.expr.LocusExpression method) write() (hail.genetics.Pedigree method) (hail.genetics.ReferenceGenome method) (hail.linalg.BlockMatrix method) (hail.MatrixTable method) (hail.Table method) (hail.vds.VariantDataset method)

write_expression() (in module hail.experimental) write_from_entry_expr() (hail.linalg.BlockMatrix static method) write_image() (hail.ggplot.GGPlot method) write_many() (hail.Table method)

X

x_contigs (hail.genetics.ReferenceGenome property)

xlab() (in module hail.ggplot)

Y

y_contigs (hail.genetics.ReferenceGenome property)

ylab() (in module hail.ggplot)

Z

zeros() (in module hail.nd)

zip() (in module hail.expr.functions) zip_with_index() (in module hail.expr.functions)