Index

Symbols

--host divbrowse-start command line option --infer-config divbrowse-start command line option --port divbrowse-start command line option

--save-config divbrowse-start command line option --version divbrowse command line option

_

__post_init__() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) __version__ (in module divbrowse) (in module divbrowse.server) _create_chrom_indices() (divbrowse.lib.genotype_data.GenotypeData method) _create_list_of_chromosomes() (divbrowse.lib.genotype_data.GenotypeData method)

_free_mem() (divbrowse.lib.genotype_data.GenotypeData method) _load_data() (divbrowse.lib.genotype_data.GenotypeData method) _load_gff3_data() (divbrowse.lib.annotation_data.AnnotationData method) _setup_sample_id_mapping() (divbrowse.lib.genotype_data.GenotypeData method) _version (in module divbrowse) (in module divbrowse._version)

A

add_stats() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) Analysis (class in divbrowse.lib.analysis) AnnotationData (class in divbrowse.lib.annotation_data)

ApiError app (in module divbrowse.wsgi) apply_variant_filter_settings() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method)

C

calc_distance_matrix() (divbrowse.lib.analysis.Analysis method) calc_distance_to_reference() (divbrowse.lib.analysis.Analysis method) calc_summary_stats (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) calc_variants_summary_stats() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) calc_variants_summary_stats_numpy() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) calc_variants_summary_stats_scikitallel() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) calcsumstats() (in module divbrowse.cli)

calculate_mean() (divbrowse.lib.variant_calls_slice.VariantCallsSlice static method) (in module divbrowse.lib.analysis) calculate_minor_allele_freq() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) calls_metadata (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) count_alternate_alleles() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) count_variants_in_window() (divbrowse.lib.genotype_data.GenotypeData method) create_app() (in module divbrowse.server)

D

divbrowse module divbrowse command line option --version divbrowse-start command line option --host --infer-config --port --save-config divbrowse._version module divbrowse.cli module divbrowse.lib module

divbrowse.lib.analysis module divbrowse.lib.annotation_data module divbrowse.lib.genotype_data module divbrowse.lib.utils module divbrowse.lib.variant_calls_slice module divbrowse.server module divbrowse.setup module divbrowse.wsgi module

E

encode() (divbrowse.lib.utils.ORJSONEncoder method)

G

gd (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) GenotypeData (class in divbrowse.lib.genotype_data) get_chromosomes() (in module divbrowse.cli) get_config_skeleton() (in module divbrowse.cli) get_data() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) get_imputed_calls() (divbrowse.lib.analysis.Analysis method)

get_nearest_gene_start_pos() (divbrowse.lib.annotation_data.AnnotationData method) get_posidx_by_genome_coordinate() (divbrowse.lib.genotype_data.GenotypeData method) get_posidx_by_genome_coordinates() (divbrowse.lib.genotype_data.GenotypeData method) get_samples_mask() (divbrowse.lib.genotype_data.GenotypeData method) get_slice_of_variant_calls() (divbrowse.lib.genotype_data.GenotypeData method) get_stats_dict() (divbrowse.lib.variant_calls_slice.VariantCallsSlice method) get_vcf_header() (divbrowse.lib.genotype_data.GenotypeData method)

I

impute_with_mean() (in module divbrowse.lib.analysis)

L

location_end (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute)

location_start (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) log (in module divbrowse)

M

main() (in module divbrowse.cli) map_input_sample_ids_to_vcf_sample_ids() (divbrowse.lib.genotype_data.GenotypeData method) map_vcf_sample_ids_to_input_sample_ids() (divbrowse.lib.genotype_data.GenotypeData method) module divbrowse divbrowse._version divbrowse.cli divbrowse.lib divbrowse.lib.analysis divbrowse.lib.annotation_data divbrowse.lib.genotype_data divbrowse.lib.utils divbrowse.lib.variant_calls_slice divbrowse.server divbrowse.setup divbrowse.wsgi

O

ORJSONEncoder (class in divbrowse.lib.utils)

P

pca() (divbrowse.lib.analysis.Analysis method) positional_lookup_success (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) positions (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute)

positions_indices (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) positions_not_found (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) print_error() (in module divbrowse.lib.utils)

R

RED (in module divbrowse.lib.utils)

RESET (in module divbrowse.lib.utils)

S

sample_ids_to_mask() (divbrowse.lib.genotype_data.GenotypeData method) samples_mask (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) samples_selected_mapped (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute)

sliced_variant_calls (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute) start() (in module divbrowse.cli) status_code (divbrowse.lib.utils.ApiError attribute) StrictEncoder (class in divbrowse.lib.utils)

T

to_dict() (divbrowse.lib.utils.ApiError method)

type_of_slice (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute)

U

umap() (divbrowse.lib.analysis.Analysis method)

V

variant_filter_settings (divbrowse.lib.variant_calls_slice.VariantCallsSlice attribute)

VariantCallsSlice (class in divbrowse.lib.variant_calls_slice) vcf2zarr() (in module divbrowse.cli)

W

with_gd() (in module divbrowse.lib.variant_calls_slice)