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

⨍ Functions 1,294◇ Types & classes 131
↓ 99 callersMethodcreate
( cls, config: Optional[PipelineConfig], name: str, task_function: Callable,
data-pipeline/src/data_pipeline/pipeline.py:118
↓ 89 callersMethodadd_task
( self, name: str, task_function: Callable, output_path: str, inputs:
data-pipeline/src/data_pipeline/pipeline.py:198
↓ 86 callersMethodget_task
(self, name: str)
data-pipeline/src/data_pipeline/pipeline.py:219
↓ 59 callersFunctionreferenceGenome
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1083
↓ 53 callersFunctionlabelForDataset
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1041
↓ 50 callersMethodget
(key: string)
graphql-api/src/queries/helpers/json-cache.ts:179
↓ 48 callersFunctiongetMetadata
( datasetId: DatasetId, fieldName: T )
dataset-metadata/metadata.ts:1032
↓ 46 callersFunctiongetCategoryFromConsequence
(consequenceTerm: any)
browser/src/vepConsequences.ts:196
↓ 46 callersMethodget_output
(self, output_name)
data-pipeline/src/data_pipeline/pipeline.py:238
↓ 41 callersMethodset
(key: string, value: T)
graphql-api/src/queries/helpers/json-cache.ts:168
↓ 38 callersFunctionsetMockApiResponses
(newResponses: MockApiResponses)
tests/__helpers__/queries.tsx:50
↓ 37 callersMethodget_output_path
(self)
data-pipeline/src/data_pipeline/pipeline.py:133
↓ 34 callersFunctionscalePosition
(...args: any[])
browser/src/ClinvarVariantsTrack/ClinvarAllVariantsPlot.spec.tsx:133
↓ 33 callersFunctiongetFlagsForContext
(context: any, variant: any)
graphql-api/src/queries/variant-datasets/shared/flags.ts:130
↓ 30 callersFunctionsimulateApiResponse
( mockedComponentName: string, query: string, children: Children, operationName: string, v
tests/__helpers__/queries.tsx:30
↓ 29 callersFunctioncreateAncestryGroupObjects
( shorthands: AncestryGroupShorthand[], includeJointFields: boolean )
browser/src/__factories__/Variant.ts:16
↓ 28 callersFunctionmakeNumericCompareFunction
(key: any)
browser/src/VariantList/sortUtilities.ts:32
↓ 27 callersFunctionfetchAllSearchResults
(client: any, searchParams: any)
graphql-api/src/queries/helpers/elasticsearch-helpers.ts:8
↓ 27 callersFunctionfieldAliasResolver
(field: any)
graphql-api/src/graphql/resolvers/aliases.ts:1
↓ 26 callersMethodinfo
(obj)
reads/src/logging.js:37
↓ 26 callersFunctionrenderNumberOrDash
(number: number)
browser/src/StatsPage/StatsPageTables/TableStyles.tsx:3
↓ 24 callersFunctionmajorConsequenceFieldResolver
(field: any)
graphql-api/src/graphql/resolvers/aliases.ts:5
↓ 24 callersFunctionrun_pipeline
(pipeline: Pipeline)
data-pipeline/src/data_pipeline/pipeline.py:257
↓ 24 callersMethodset_outputs
(self, outputs)
data-pipeline/src/data_pipeline/pipeline.py:232
↓ 22 callersFunctionlogButtonClick
(eventLabel: string)
browser/src/analytics.ts:16
↓ 22 callersFunctionrenderRoundedNumber
( num: number | null, { precision = 1 as number, tooltipPrecision = 3, highlightColor = null a
browser/src/ConstraintTable/constraintMetrics.tsx:15
↓ 19 callersFunctionmakeMockClient
(response: any)
graphql-api/src/queries/structural-variant-queries.spec.ts:50
↓ 18 callersMethodfocusItem
(itemId: any)
browser/src/DatasetSelector.tsx:344
↓ 18 callersFunctionisSexSpecificPopulation
(pop: any)
browser/src/VariantPage/PopulationsTable.tsx:55
↓ 18 callersFunctionkubectl
(args: typing.List[str], **kwargs)
deploy/deployctl/shell.py:29
↓ 18 callersFunctionmergeOverlappingRegions
(sortedRegions: any)
graphql-api/src/queries/helpers/region-helpers.ts:22
↓ 17 callersFunctionforAllDatasets
( contextDescription: string, tests: (datasetId: DatasetId) => void )
tests/__helpers__/datasets.tsx:4
↓ 17 callersFunctionresponseWithHits
(hits: any[])
graphql-api/src/queries/structural-variant-queries.spec.ts:24
↓ 16 callersFunctionisVariantId
(str)
reads/src/schema.js:173
↓ 16 callersFunctiontruncate
(str: any, maxLength = 5)
browser/src/VariantCooccurrencePage/VariantCooccurrenceDetailsTable.tsx:34
↓ 15 callersMethoderror
(obj)
reads/src/logging.js:49
↓ 15 callersFunctionminimalHit
(freq: any)
graphql-api/src/queries/structural-variant-queries.spec.ts:40
↓ 15 callersFunctionmockQueries
()
tests/__helpers__/queries.tsx:26
↓ 15 callersFunctionresetMockApiCalls
()
tests/__helpers__/queries.tsx:58
↓ 15 callersFunctionresetMockApiResponses
()
tests/__helpers__/queries.tsx:54
↓ 15 callersFunctionsubset_table
(ds)
data-pipeline/src/data_pipeline/helpers/datasets_config.py:36
↓ 15 callersFunctionvariant_id
Expression for computing <chrom>-<pos>-<ref>-<alt>. Assumes alleles were split. Args: max_length: (optional) length at which to trun
data-pipeline/src/data_pipeline/data_types/variant/variant_id.py:8
↓ 15 callersFunctionx_position
(locus: hl.expr.LocusExpression)
data-pipeline/src/data_pipeline/data_types/locus.py:17
↓ 14 callersFunctionassertDatasetAndReferenceGenomeMatch
(datasetId: any, referenceGenome: any)
graphql-api/src/queries/helpers/validation-helpers.ts:4
↓ 14 callersFunctionfetchSearchResults
( datasetId: DatasetId, query: string )
browser/src/search.ts:79
↓ 14 callersFunctionisSexSpecificPopulation
(pop: Subpopulation)
browser/src/CopyNumberVariantPage/CNVPopulationsTable.tsx:48
↓ 14 callersFunctionisV4
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1095
↓ 14 callersFunctionmakeStringCompareFunction
(key: any)
browser/src/VariantList/sortUtilities.ts:29
↓ 13 callersFunctionformatClinvarDate
(dateString: any)
browser/src/ClinvarVariantsTrack/formatClinvarDate.ts:4
↓ 13 callersFunctiongetFilteredRegions
(exons: Exon[])
graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts:413
↓ 13 callersFunctionnormalized_contig
(contig: hl.expr.StringExpression)
data-pipeline/src/data_pipeline/data_types/locus.py:4
↓ 12 callersFunctionfilterVariantsInZoomRegion
(variants: any, zoomRegion: any)
browser/src/RegionViewer/filterVariantsInZoomRegion.ts:4
↓ 12 callersFunctionisEmpty
(val: any)
browser/src/VariantList/sortUtilities.ts:3
↓ 11 callersFunctionforDatasetsMatching
( inclusionPattern: RegExp, contextDescription: string, tests: (datasetId: DatasetId) => void )
tests/__helpers__/datasets.tsx:11
↓ 11 callersFunctiongetLabelForConsequenceTerm
(consequenceTerm: any)
browser/src/vepConsequences.ts:198
↓ 11 callersFunctiontextOrMissingTextWarning
( entityType: string, textMapping: Record<string, string>, key: string )
browser/src/missingContent.ts:1
↓ 11 callersMethodwarn
(obj)
reads/src/logging.js:43
↓ 10 callersFunctionfetchStructuralVariantById
( esClient: any, datasetId: SvDatasetId, variantId: string )
graphql-api/src/queries/structural-variant-queries.ts:57
↓ 10 callersFunctionfreq
(ds, *args, **kwargs)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_variants.py:25
↓ 10 callersFunctionfreq
(ds, *args, **kwargs)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:26
↓ 10 callersFunctionwithSize
(_options: any)
tests/__mocks__/react-sizeme.ts:14
↓ 9 callersMethodadd_download_task
(self, name, *args, **kwargs)
data-pipeline/src/data_pipeline/pipeline.py:214
↓ 9 callersFunctionfn
(variant)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:481
↓ 9 callersFunctionfreq_joint
(ds, subset=None, pop=None, sex=None, raw=False)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:324
↓ 9 callersFunctionlogScaleMetrics
(selectedMetric: string)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:559
↓ 9 callersFunctionmergeExomeAndGenomeData
({ datasetId, variants, preferJointData = false, }: { datasetId?: DatasetId variants: Variant[] pr
browser/src/VariantList/mergeExomeAndGenomeData.ts:125
↓ 9 callersFunctionwithCache
( fn: AsyncCacheFunction, keyFn: keyFunction, options: WithCacheOptions = {} )
graphql-api/src/cache.ts:82
↓ 8 callersFunctionadd
(n1: number | null | undefined, n2: number | null | undefined)
browser/src/VariantList/mergeExomeAndGenomeData.ts:7
↓ 8 callersFunctionadd_variant_document_id
(ds)
data-pipeline/src/data_pipeline/helpers/datasets_config.py:40
↓ 8 callersMethodcanLoadMoreTracks
(exomeOrGenome: SequencingType, category: TrackCategory)
browser/src/ReadData/ReadData.tsx:273
↓ 8 callersFunctionformatTooltip
(bin: any, includedCategories: IncludedCategories)
browser/src/ClinvarVariantsTrack/ClinvarBinnedVariantsPlot.tsx:42
↓ 8 callersFunctionisV2
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1091
↓ 8 callersFunctionisV3
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1093
↓ 8 callersFunctionmergeExomeGenomeAndJointPopulationData
({ datasetId, exomePopulations = [], genomePopulations = [], jointPopulations = null, }: { datasetId
browser/src/VariantList/mergeExomeAndGenomeData.ts:43
↓ 8 callersFunctionnullifyEmptyObject
(field: any)
graphql-api/src/graphql/resolvers/gene-fields.ts:8
↓ 8 callersFunctiontruncate
(str: any, maxLength = 5)
browser/src/VariantCooccurrencePage/VariantCooccurrenceHaplotypeCountsTable.tsx:23
↓ 7 callersMethodexists
(self, path)
data-pipeline/src/data_pipeline/pipeline.py:36
↓ 7 callersFunctionfetchStructuralVariantsByRegion
( esClient: any, datasetId: SvDatasetId, region: RegionQueryParams )
graphql-api/src/queries/structural-variant-queries.ts:167
↓ 7 callersFunctiongetPredictorValue
(variant: VariantTableVariant, id: string)
browser/src/VariantList/ExportVariantsButton.tsx:133
↓ 7 callersMethodget_inputs
(self)
data-pipeline/src/data_pipeline/pipeline.py:139
↓ 7 callersFunctionhasStructuralVariants
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1070
↓ 7 callersFunctionisExac
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1097
↓ 7 callersFunctionmockApiCalls
()
tests/__helpers__/queries.tsx:56
↓ 7 callersMethodwrite
(self, path, overwrite=False)
data-pipeline/tests/pipeline/test_config.py:62
↓ 6 callersFunctionannotateVariantsWithClinvar
(variants: any, clinvarVariants: any)
browser/src/VariantList/annotateVariantsWithClinvar.ts:1
↓ 6 callersFunctioncoverageDatasetId
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1136
↓ 6 callersFunctionfetchCoverage
(esClient: any, { index, contig, regions, bucketSize }: any)
graphql-api/src/queries/coverage-queries.ts:35
↓ 6 callersFunctionformatCoverageBins
(bins: any)
graphql-api/src/graphql/resolvers/coverage.ts:9
↓ 6 callersFunctionformatMetricValue
(value: number, metric: string, isLog: boolean)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:564
↓ 6 callersFunctiongetConsequenceForContext
(context: any)
graphql-api/src/queries/variant-datasets/shared/transcriptConsequence.ts:1
↓ 6 callersFunctionhasCopyNumberVariants
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1073
↓ 6 callersFunctionisGene
(geneOrTranscript: Gene | Transcript)
browser/src/ConstraintTable/ConstraintTable.tsx:18
↓ 6 callersMethodrenderColumnHeader
(key: any, label: any, tooltip: any)
browser/src/MitochondrialVariantPage/MitochondrialVariantHaplogroupFrequenciesTable.tsx:75
↓ 6 callersMethodrenderColumnHeader
({ key, label, tooltip = null, props = {} }: any)
browser/src/VariantPage/PopulationsTable.tsx:151
↓ 6 callersMethodrenderLoadMoreButton
(exomeOrGenome: any, category: any)
browser/src/ReadData/ReadData.tsx:367
↓ 6 callersFunctionrenderTeamMembers
(members: TeamMember[])
browser/src/TeamPage/TeamPage.tsx:62
↓ 6 callersFunctionstringCompareFunction
(key: Key)
browser/src/useTableSort.tsx:96
↓ 6 callersFunctionvalidate_rows
(ht: hl.Table, cls: object)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_validation.py:25
↓ 6 callersFunctionvariantFeedbackUrl
(variant: any, datasetId: any)
browser/src/variantFeedback.ts:4
↓ 6 callersFunctionzoomedRegion
(region: any, zoom: any)
browser/src/RegionPage/RegionControls.tsx:45
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