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

_

__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)

_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

AnnotationData (class in divbrowse.lib.annotation_data) ApiError

app (in module divbrowse.wsgi) apply_variant_filter_settings() (divbrowse.lib.genotype_data.GenotypeData method)

C

calc_pca_for_slice_of_variant_calls() (in module divbrowse.lib.genotype_data) calc_umap_for_slice_of_variant_calls() (in module divbrowse.lib.genotype_data) calc_variants_summary_stats() (divbrowse.lib.genotype_data.GenotypeData method) calcsumstats() (in module divbrowse.cli)

calculate_mean() (in module divbrowse.lib.genotype_data) calculate_minor_allele_freq() (divbrowse.lib.genotype_data.GenotypeData method) count_alternate_alleles() (divbrowse.lib.genotype_data.GenotypeData 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.annotation_data module divbrowse.lib.genotype_data module divbrowse.lib.utils module divbrowse.server module divbrowse.setup module divbrowse.wsgi module

G

GenotypeData (class in divbrowse.lib.genotype_data) get_chromosomes() (in module divbrowse.cli) get_config_skeleton() (in module divbrowse.cli) get_nearest_gene_start_pos() (divbrowse.lib.annotation_data.AnnotationData method)

get_posidx_by_genome_coordinate() (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_vcf_header() (divbrowse.lib.genotype_data.GenotypeData method)

I

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

L

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.annotation_data divbrowse.lib.genotype_data divbrowse.lib.utils divbrowse.server divbrowse.setup divbrowse.wsgi

P

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) 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)

V

vcf2zarr() (in module divbrowse.cli)