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Functions1,294 in github.com/broadinstitute/gnomad-browser

⨍ Functions 1,294◇ Types & classes 131
↓ 2 callersFunction_prepare_genotype_distribution
(allele_scatter_plot_histogram)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_short_tandem_repeats.py:115
↓ 2 callersFunction_set_field_parameter
(mapping, field, parameter, value)
data-pipeline/src/data_pipeline/helpers/elasticsearch_export.py:57
↓ 2 callersFunctionaddDefaultVariantCooccurrenceCounts
(gene: any)
graphql-api/src/graphql/resolvers/gene.ts:8
↓ 2 callersFunctionaddMissingAncestries
( currentAncestries: Population[], versionAncestries: PopulationId[] )
browser/src/VariantList/mergeExomeAndGenomeData.ts:26
↓ 2 callersFunctionadvanceOverIntervals
( intervals: Interval[], distance: number, strand: Strand )
browser/src/ClinvarVariantsTrack/ClinvarAllVariantsPlot.tsx:85
↓ 2 callersFunctionageRangeLabel
(ageRange: [number | null, number | null])
browser/src/ShortTandemRepeatPage/ShortTandemRepeatAgeDistributionPlot.tsx:24
↓ 2 callersFunctionaggregate_counts
(counts)
data-pipeline/src/data_pipeline/pipelines/variant_cooccurrence_counts.py:63
↓ 2 callersFunctionbuildCounts
( severities: readonly VariantCooccurrenceSeverity[], afCutoffs: readonly VariantCooccurrenceAfCutoff[],
browser/src/__factories__/VariantCooccurrenceCountsPerSeverityAndAf.ts:45
↓ 2 callersFunctionbuildWhere
({ id, filter })
reads/src/resolveShortTandemRepeatReads.js:6
↓ 2 callersFunctioncalculateAF
(ac: number, an: number)
browser/src/MitochondrialVariantPage/MitochondrialVariantHaplogroupFrequenciesTable.tsx:56
↓ 2 callersFunctioncalculatePopAF
(ac: number, an: number)
browser/src/VariantPage/PopulationsTable.tsx:61
↓ 2 callersFunctioncalculatePopSF
(sc: number, sn: number)
browser/src/CopyNumberVariantPage/CNVPopulationsTable.tsx:51
↓ 2 callersFunctionclinvarVariantClinicalSignificanceCategory
(variant: any)
browser/src/ClinvarVariantsTrack/clinvarVariantCategories.ts:51
↓ 2 callersFunctioncohortDescription
( subsetId: string | undefined, frequencyField: 'exome' | 'genome' )
graphql-api/src/graphql/resolvers/va.ts:218
↓ 2 callersFunctioncompressed_variant_id
(locus: hl.expr.LocusExpression, alleles: hl.expr.ArrayExpression)
data-pipeline/src/data_pipeline/data_types/variant/variant_id.py:68
↓ 2 callersFunctionconsequence_term_rank
(consequence_term)
data-pipeline/src/data_pipeline/data_types/variant/transcript_consequence/vep.py:52
↓ 2 callersFunctionconsolidatedFlags
(row: any)
browser/src/VariantList/variantTableColumns.tsx:51
↓ 2 callersFunctioncreateInSilicoPredictorsList
(variant: any)
graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts:260
↓ 2 callersFunctioncreatePopulationColumns
(datasetId: DatasetId)
browser/src/VariantList/ExportVariantsButton.tsx:34
↓ 2 callersFunctioncreateUnlimitedElasticClient
()
graphql-api/src/elasticsearch.ts:28
↓ 2 callersFunctioncreateVersionSpecificColumns
(datasetId: DatasetId)
browser/src/VariantList/ExportVariantsButton.tsx:171
↓ 2 callersFunctiondebounce
(fn: (...args: any[]) => void)
tests/__mocks__/lodash.debounce.ts:4
↓ 2 callersFunctionelasticsearch_mapping_for_table
Creates an Elasticsearch mapping definition for a Hail table's row value type. https://www.elastic.co/guide/en/elasticsearch/guide/current/r
data-pipeline/src/data_pipeline/helpers/elasticsearch_export.py:66
↓ 2 callersFunctionesFieldsToFetch
(subset: any)
graphql-api/src/queries/structural-variant-queries.ts:107
↓ 2 callersFunctionesFieldsToFetch
()
graphql-api/src/queries/copy-number-variant-queries.ts:63
↓ 2 callersFunctionestimateHaplotypeCounts
(genotypeCounts: any)
graphql-api/src/queries/variant-cooccurrence-queries.ts:203
↓ 2 callersFunctionexomeLegendText
(exomeMetricValue: number, selectedMetric: string)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:990
↓ 2 callersFunctionfetchGeneSymbolSearchResults
(query: string, referenceGenome: ReferenceGenome)
browser/src/search.ts:16
↓ 2 callersFunctionfetchIndexMetadata
(esClient: any, index: any)
graphql-api/src/queries/helpers/elasticsearch-helpers.ts:48
↓ 2 callersFunctionfetchLocalAncestryPopulationsByVariant
( esClient: any, datasetId: any, variantId: any )
graphql-api/src/queries/local-ancestry-queries.ts:8
↓ 2 callersFunctionfetchMitochondrialGenomeCoverage
( esClient: any, { index, regions, bucketSize }: any )
graphql-api/src/queries/mitochondrial-coverage-queries.ts:18
↓ 2 callersFunctionfetchTrackCallableCoverage
(esClient: any, { regions }: any)
graphql-api/src/queries/cnv-coverage-queries.ts:17
↓ 2 callersFunctionfetchVariantById
(esClient: any, datasetId: DatasetId, variantIdOrRsid: any)
graphql-api/src/queries/variant-queries.ts:118
↓ 2 callersFunctionfile_exists
(path)
data-pipeline/src/data_pipeline/pipeline.py:44
↓ 2 callersFunctionfilterCopyNumberVariantsInZoomRegion
( copyNumberVariants: CopyNumberVariant[], zoomRegion: any )
browser/src/RegionViewer/filterVariantsInZoomRegion.ts:28
↓ 2 callersFunctionfilterStructuralVariantsInZoomRegion
(structuralVariants: any, zoomRegion: any)
browser/src/RegionViewer/filterVariantsInZoomRegion.ts:16
↓ 2 callersFunctionfilter_by_af_cutoff
(counts, af_cutoffs)
data-pipeline/src/data_pipeline/pipelines/variant_cooccurrence_counts.py:70
↓ 2 callersFunctionfindSubcohortIds
(cohortId: string, possibleSubcohortIds: string[])
graphql-api/src/graphql/resolvers/va.ts:299
↓ 2 callersFunctionformatVariantQualityMetrics
(qualityMetrics: any)
graphql-api/src/queries/variant-datasets/gnomad-v2-variant-queries.ts:55
↓ 2 callersFunctiongcloud
(args: typing.List[str], **kwargs)
deploy/deployctl/shell.py:7
↓ 2 callersFunctiongenomeLegendText
(genomeMetricValue: number, selectedMetric: string)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:998
↓ 2 callersFunctiongetAFBin
({ sequencingType, ac, an, }: { sequencingType: 'exome' | 'genome' ac: numbe
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:268
↓ 2 callersFunctiongetAncestryAndSexIds
(subsetId: string)
graphql-api/src/graphql/resolvers/va.ts:213
↓ 2 callersFunctiongetAvailableMetrics
(datasetId: any)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:460
↓ 2 callersFunctiongetCategoryCounts
(variant: any)
graphql-api/src/queries/variant-cooccurrence-queries.ts:85
↓ 2 callersFunctiongetConsequenceColor
(consequenceTerm: any)
browser/src/MNVPage/MNVConsequence.tsx:16
↓ 2 callersFunctiongetCooccurrencePattern
(cooccurrenceData: CooccurrenceForPopulation)
browser/src/VariantCooccurrencePage/VariantCooccurrenceSummaryTable.tsx:16
↓ 2 callersFunctiongetDataCategories
(dataRow)
browser/src/StatsPage/StackedBarGraph.tsx:102
↓ 2 callersFunctiongetDefaultSearchDataset
(selectedDataset: any)
browser/src/Searchbox.tsx:30
↓ 2 callersFunctiongetFilteredVariants
( filter: VariantFilterState, variants: Variant[], variantTableColumns: VariantTableColumn[] )
browser/src/VariantList/filterVariants.ts:23
↓ 2 callersFunctiongetGlobalFrameshiftCoordinates
( variant: ClinvarVariant, transcript?: Transcript )
browser/src/ClinvarVariantsTrack/ClinvarAllVariantsPlot.tsx:23
↓ 2 callersFunctiongetMetricValueX
(metricValue: any)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:759
↓ 2 callersFunctiongetPlotRegions
(expressionRegions: any, getValueForRegion: any)
browser/src/GenePage/TissueExpressionTrack.tsx:25
↓ 2 callersFunctiongetProbabilityCompoundHeterozygous
(haplotypeCounts: any)
graphql-api/src/queries/variant-cooccurrence-queries.ts:224
↓ 2 callersMethodget_all_task_names
(self)
data-pipeline/src/data_pipeline/pipeline.py:225
↓ 2 callersFunctionget_data_environment
(env_value: str)
data-pipeline/src/data_pipeline/config.py:10
↓ 2 callersFunctionget_k8s_deployments
(selector: str)
deploy/deployctl/shell.py:38
↓ 2 callersFunctionget_most_recent_k8s_deployment
(selector: str)
deploy/deployctl/shell.py:53
↓ 2 callersFunctionget_most_recent_tag
(gcr_image_repository: str)
deploy/deployctl/shell.py:14
↓ 2 callersFunctionget_n_columns
(table)
data-pipeline/src/data_pipeline/pipelines/check_missingness.py:10
↓ 2 callersMethodget_output_path
(self)
data-pipeline/src/data_pipeline/pipeline.py:70
↓ 2 callersFunctiongroupConsequences
( consequences: TranscriptConsequence[], key: 'major_consequence' | 'gene_id' )
browser/src/MitochondrialVariantPage/MitochondrialVariantTranscriptConsequenceList.tsx:15
↓ 2 callersFunctiongroupConsequences
(consequences: any, key: any)
browser/src/VariantPage/TranscriptConsequenceList.tsx:15
↓ 2 callersFunctionhasNonCodingConstraints
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1048
↓ 2 callersFunctionhasShortVariants
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1068
↓ 2 callersFunctionhasV2Genome
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1101
↓ 2 callersFunctionhasVariantCoocurrence
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1045
↓ 2 callersFunctionhashWithSha512t24u
(s: string)
graphql-api/src/graphql/resolvers/va.ts:114
↓ 2 callersFunctionimage_exists
(gcr_image_repository: str, tag: str)
deploy/deployctl/shell.py:21
↓ 2 callersFunctionimport_structural_variants
(vcf_path)
data-pipeline/src/data_pipeline/datasets/gnomad_sv_v2.py:71
↓ 2 callersFunctionincreaseRateLimitCounter
(key: any, value: any)
graphql-api/src/graphql/rate-limiting.ts:23
↓ 2 callersFunctioninterleaveReads
(allVariantReads: any)
browser/src/ReadData/ReadData.tsx:476
↓ 2 callersFunctionisAdjacentRepeat
( obj: ShortTandemRepeat | ShortTandemRepeatAdjacentRepeat )
browser/src/ShortTandemRepeatPage/shortTandemRepeatHelpers.ts:202
↓ 2 callersFunctionisCisSingleton
(genotype_counts: GenotypeCounts)
browser/src/VariantCooccurrencePage/VariantCooccurrencePage.tsx:170
↓ 2 callersFunctionisRejected
(promise: PromiseSettledResult<unknown>)
graphql-api/src/esPoll.ts:11
↓ 2 callersFunctionisRepunitSelectionPathogenic
( selectedRepeatUnits: string[] | null, selectionIndex: number )
browser/src/ShortTandemRepeatPage/ShortTandemRepeatPage.tsx:294
↓ 2 callersFunctionisSubset
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1039
↓ 2 callersFunctionisV3Subset
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1089
↓ 2 callersFunctionisV4SVs
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1142
↓ 2 callersFunctionk8s_deployment_exists
(k8s_deployment_name: str)
deploy/deployctl/shell.py:60
↓ 2 callersFunctionlegendLabel
(colorBy: ColorBy, key: string)
browser/src/ShortTandemRepeatPage/ShortTandemRepeatAlleleSizeDistributionPlot.tsx:109
↓ 2 callersMethodload
(self)
deploy/deployctl/config.py:36
↓ 2 callersMethodloadData
()
browser/src/Query.tsx:84
↓ 2 callersFunctionlogScaleAllowed
(colorBy: ColorBy | null)
browser/src/ShortTandemRepeatPage/ShortTandemRepeatPage.tsx:151
↓ 2 callersFunctionmakeClinvarCompareFunction
(key: any)
browser/src/VariantList/sortUtilities.ts:35
↓ 2 callersFunctionmodified_time
(path)
data-pipeline/src/data_pipeline/pipeline.py:50
↓ 2 callersFunctionnullifyEmptyObject
(field: any)
graphql-api/src/graphql/resolvers/clinvar-variant-fields.ts:3
↓ 2 callersFunctionnullify_nan
(value)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_variants.py:8
↓ 2 callersFunctionnullify_nan
(value)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:8
↓ 2 callersFunctiononClickVariant
(...args: any[])
browser/src/ClinvarVariantsTrack/ClinvarAllVariantsPlot.spec.tsx:134
↓ 2 callersFunctionoutput_region
(region)
data-pipeline/src/data_pipeline/data_types/pext.py:115
↓ 2 callersFunctionparseGeneSearchResults
( response: GeneSearchResult, query: string, datasetId: DatasetId, startingGeneSymbolCounts: Record<st
browser/src/search.ts:36
↓ 2 callersFunctionprepareData
({ includeExomes, includeGenomes, includeLargerBin = false, samples, selectedMetric, variant, }: a
browser/src/VariantPage/VariantGenotypeQualityMetrics.tsx:27
↓ 2 callersFunctionprepare_gnomad_v2_variants_helper
(path, exome_or_genome)
data-pipeline/src/data_pipeline/datasets/gnomad_v2/gnomad_v2_variants.py:95
↓ 2 callersFunctionprepare_gnomad_v4_variants_helper
(input_path: str, exomes_or_genomes: str)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:18
↓ 2 callersFunctionprepare_variant_cooccurrence_counts
(tsv_path, field_name_map)
data-pipeline/src/data_pipeline/pipelines/variant_cooccurrence_counts.py:27
↓ 2 callersFunctionprintAAorNA
(aa: string | null)
browser/src/RegionalMissenseConstraintTrack.tsx:112
↓ 2 callersFunctionprint_pool_name
(pool: str)
deploy/deployctl/subcommands/browser_deployments.py:133
↓ 2 callersFunctionregionColor
(region: any)
browser/src/RegionalGenomicConstraintTrack.tsx:45
↓ 2 callersMethodrender
()
browser/src/Query.tsx:136
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